ISSN: 2822-0838 Online

The Frequencies of Allele Distribution of CYP2C9 and CYP2C19 Gene Polymorphisms in Healthy Papuan Population, Indonesia

Syahrul Tuba*, Zullies Ikawati, and Mustofa
Published Date : 2021-05-18
Journal Issues : Number 3, July-September 2021

Abstract This study's objective was to determine the distribution of allele frequencies of CYP2C9 and CYP2C19 gene polymorphisms among the Papuan population, known as the second-largest ethnic group in Indonesia. According to recent research, there is a decrease in CYP2C9 and CYP2C19 produced by humans globally, including in Indonesia. These gene polymorphisms aid in the transmission of various endogenous and exogenous drugs in the human body. Material and Methods: A sum of 99 subjects, comprising 73 male and 26 female subjects aged 20-30 years, were used for this research. PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) analysis using AvaII, NsiI, and SfaNI enzymes tested for the genotypes CYP2C9 and CYP2C19 administered. The distribution of genotypes was calculated in the population (P<0.05) using the Hardy-Weinberg equilibrium. The Faculty of Medicine Gadjah Mada University's Medical and Health Research Ethics Committee (MHREC) accepted this research with written consent. The results revealed that in Papua subjects, CYP2C9*2 (rs1799853) and CYP2C19*17 (rs12248560) alleles were absent while in 17 percent of the population CYP2C9*3 (rs1057910) allele frequency was. In conclusion, CYP2C9*3 has the highest polymorphism rate in Indonesia, with the absence of CYP2C9*2 and CYP2C19*17. Therefore, genetic drift can occur within this ethnic group.


Keywords: Genotyping; Papuan ethnic; Pharmacogenetics; Polymorphisms


Funding: This work is supported by a grant from the LPDP scholarship Ministry of Finance of Indonesia for support and cooperation. 


Citation: Tuba, S., Ikawati, Z., and Mustofa, 2021. The frequencies of allele distribution of CYP2C9 and CYP2C19 gene polymorphisms in healthy papuan population, Indonesia. CMUJ. Nat. Sci. 20(3): e2021066



The Papuan Past Project incorporates archaeological and genomic approaches to investigate the biological, cultural, and technological evolution of the human population occupation and adaptation modalities over the last 50,000 years. The ambiguity of the genetic environment present in Papuan populations has been explained by recent human genetic studies (, accessed by 18 February 2021).


Variations in drug response among various people/populations are influenced by several factors, including differences in allele frequency of single nucleotide polymorphisms (SNPs) that affect drug-response genes functionally (Bachtiar et al., 2019). There were 70,187 adverse drug reactions (ADRs) cases, according to the 2007–2009 US FDA Adverse Event Reporting System (FAERS).


The CYP450 enzyme system's ability metabolism differs in all populations (Mcgraw & Waller, 2012). The CYP450 cytochrome group is thought to have an important role as a metabolizer of a phase I reaction drug that oxidizes over 90% of the drug. Over 90% of the oxidizing drug is identified with CYP1A2, 2A6, 2C9, 2C19, 2E1, 2D6, and 3A4 (Rendic & Guengerich, n.d.). One of the subfamilies of CYP2C is CYP2C9, a significant P450 cytochrome protein with an important function in oxidating xenobiotics and endogenous drugs. CYP2C9 can process around 100 remedial medications, for example, a limited restorative record including warfarin, phenytoin, and routinely endorsed medications, acenocoumarin, tolbutamide, losartan, glipizide, and some nonsteroidal calming drugs (Rettie & Jones, 2005). CYP2C9 and CYP2C19 genes have different capabilities in metabolizing individual drugs in the human body(Xie et al., 2002). Cytochrome P450 2C9 (CYP2C9) is an enzyme found in the human body encoded by the CYP2C9 gene (Romkes et al., 1993). These two subfamilies have a potent polymorphism in the human body, especially in the liver (Zanger & Klein, 2013). The second most noteworthy protein among all CYP isoforms is CYP2C9 and is integral to the digestion of numerous xenobiotics and different endogenous (Soares et al., 2008).


Currently, there are more than 60 alleles that have been identified in the human gene CYP2C9 (*1A to *60) (Lazar et al., 2004). The CYP2C9*2 gene is a mutation (missense mutation) 430 T > C that causes R144C substitution associated with decreased CYP2C9 substrate enzyme activity. CYP2C9*3 is a mutation (missense mutation) 1075 A > C on exon 7, which causes I359L substitution at the CYP2C9 active point and is directly involved in the substrate. The performance of both CYP2C9*2 and CYP2C9*3 polymorphisms varies between communities. Not only are differences in the prevalence of each polymorphism, but one type may be more dominant than others. In the Caucasian population, the prevalence of CYP2C9*2 polymorphism varies from 8 to 19.1% and is higher than the native population of Canada, Afro-American and Asian (Table 1) (Saberi et al., 2020).


Table 1. The prevalence of CYP2C9 polymorphs among different ethnic groups.







Point mutation










Aborigine Canada















Note:  nd=not determined


Conversely, CYP2C9*3 polymorphism is more common in Asian populations (1.7-5 percent) than CYP2C9*2 (0 percent) polymorphism. The prevalence of CYP2C9*3 polymorphisms in Asia is still much lower than in the Caucasian population (6-10 percent). CYP2C19 is a quality that assumes a significant function in the digestion of 25 significant sorts of medications, including psychotropic medications, proton inhibitor pump, and anticonvulsants, and accommodates the leeway of certain key medications, for example, S-mephenytoin, diazepam, omeprazole, proguanil, and R-warfarin (Scordo et al., 2001; Rosemary & Adithan, 2007). At present, more than 49 alleles in the CYP2C19 quality have been recognized and portrayed, including CYP2C19*17, which increment chemical movement. CYP2C19*17 allele, with ultra-rapid metabolizer (UM) (Li-wan-po et al., 2010). This quality was somewhere in the range of 18 and 27 percent of the European population between 0.15-0.44 percent in Asia and 10 to 27 percent in Africa. The CYP2C19*17 allele is firmly connected to a decrease in serum concentration of Pantoprazole (Gawroñska-Szklarz et al., 2012). Likewise has this impact on pharmaceutical medicines such as escitalopram, clopidogrel, and voriconazole (Hirota et al., 2013).


CYP2C9 and CYP2C19 have primarily been carried out in polymorphic research in the Americas and the Caucasus and even in the East Asian (i.e., Chinese, Japanese, or Korean) populations. There is limited research on CYP2C9 and CYP2C19 in Southeast Asia. One work in the Indonesian community (Buginese in the South Sulawesi province) has been performed. This study was the first time to do in Papuan ethnic in Indonesia and to determine the Papuan population's genetic polymorphism. We hope to be able to conduct rigorous study for the next research about polymorphism genetics and toxicity in the Clinical Setting. 



In this study conducted in 2018, a total was collected whole blood samples of 99 healthy subjects (73 males and 26 females, aged 20-30 years old) and Papuan ethnicity determined from 3 descendants and above are origin ethnic Papuans (father-mother, grandparents, great-grandparents). All participants were healthy as described by medical history, physical examination, told them (both verbally and in writing), experimental procedures, and the study's purposes. According to the manufacturer's protocol, genetic DNA was extracted from blood samples by Genomic DNA Mini Kit (Blood) Blood Protocol (Geneaid, USA). Genotyping for CYP2C9*2 (rs1799853, 430C>T)), CYP2C9*3 (rs1057910, 1075A>C), CYP2C19*17 (rs12248560, 806C>T) determined by techniques of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods. AvaII, NsiI, and SfaNI, respectively, have been used as restriction enzymes were obtained from New England Biolabs (Hitchin, UK). The distribution of genotypes was carried out by Hardy-Weinberg Equilibrium analysis to compare the observed and expected genotype frequencies using the chi-square test in the population (P<0.05).


Written informed consent for their involvement in the study was obtained from all of them and approved protocol by The Medical and Health Research Ethics Committee (MHREC), Faculty of Medicine, Gadjah Mada University (KE/FK/0105/EC/2018).


CYP2C9 and CYP2C19 Genotyping Procedures

PCR-RFLP analysis was performed to identify the CYP2C9*2 (rs1799853, 430C>T)), CYP2C9*3 (rs1057910, 1075A>C), CYP2C19*17 (rs12248560, 806C>T). In brief (Table 2), PCR was done in a 50-μl last response volume including 2.5 mM MgCl2, ten mM Tris-HCl, 50 mM KCl, ten mM dNTPs, 1.5 µL of AmpliTaq DNA polymerase, and around 200 ng of human genomic DNA, and the groundwork (0.32 μM). Aliquots of each PCR item (15 μl) were exposed to limitation catalyst examination with five µL of AvaII (CYP2C9*2), NsiI (CYP2C9*3), and SfaNI (CYP2C19*17) separately. Processed items detached by electrophoresis utilizing a 4 percent agarose gel after hatching at 70° C for around an hour.



Table 2. The condition about studied genes in the present study.


Primer sequences

Annealing temperature

Restriction enzyme

Digestion products (bp)





60.6 0C


Wild (CC): 454 Mutant (TT): 57, 397



F: 5’TgCACgAggTCCAgAgATgC 3’


59 0C


W (AA): 168 M (CC): 50, 118




57.2 0C


W (CC): 165 M (TT): 20, 145

Note: bp=base pare


Statistical Analysis

Deviation from Hardy-Weinberg Equilibrium (HWE) tested using the online calculator (Rodriguez et al., 2009). Allele frequencies of various genotypes were compared using the x2 test. P-value of < 0.05 considered statistically significant



This study was the second time in the Indonesian population to test genetic polymorphism. The first was the Buginese population and the second for the Papuan population to assess the genes' genotype and genetic polymorphism CYP2C9 and CYP2C19. The most common allele found in the Papuan population was CYP2C9*3. The CYP2C9*3 allele frequency was 17 percent in stable Papuan subjects. Determination of the genotype showed that 68 of the PM were homozygous for C / C (69.4%), 27 were heterozygous for carrier A/C (27.6%), and three were wild for A/A (3%) (Table 3). Hence, the most popular allele is CYP2C9*3 (rs1057910, 1075A>C) in the Papuan population. From the 98 subjects present in this study, CYP2C9*2 (rs1799853, 430C>T) and CYP2C19*17 (rs12248560, 806C>T) alleles were missing.


Table 3. The frequency of genotypes and alleles of CYP2C9 and CYP2C19 Papua subjects  (n = 98)

Polymorphism CYP2C9 and CYP2C19


Genotypes frequency %
(95% CI)

Allele frequency % (95% CI)







(rs1799853, 430C>T)




0 (0)

0 (0)

98 (100)





100 (0)




(rs1057910, 1075A>C)




3 (3,06)

27 (27,55)

68 (69,39)



0,17 (17)

0,83 (83)



(rs12248560, 806C > T)




0 (0)

0 (0)

98 (100)




100 (0)




This research is the first to identify polymorphism in Papuan ethnicity, East Indonesia. Indonesia, an archipelago country in Southeast Asia, consisting of a variety of different ethnic groups. The database of gene polymorphisms encoding CYP2C9 and CYP2C19 enzyme protein expression in indigenous Indonesian tribes is still limited. One of the largest indigenous ethnic groups exists in Papua. This tribe is the second largest tribe in Indonesia after the Java tribe, with a phenotype and socio-cultural distinct from other tribes in Indonesia. The genetic drift of Papua's population could be a high differentiation between Indonesia's other ethnic groups.


The island of Papua located in Eastern Indonesia haves a unique characteristic to identify genetics ancestry in this reflects Austronesian migrations (, accessed by 18 February 2021). Previous study involved Asian and Papuan genetic drift related to the mtDNA and Y-Chromosome (Wollstein et al., 2010; Reich et al., 2011). However, none of the previous polymorphism genetics of East Indonesia studied to apply in Clinical Setting. 


The ancient migration wave was thought to have carried the ancestors of many "Australoid" groups in Southeast Asia and Australia, including the Papuans and Australian Aboriginals and any communities in the Andaman Philippines. The collective is known as Negritos in West Malaysia (Chisholm, 1995). Genetics Papuan ancestry is part of a New Guinea based on mtDNA and Y-chromosome studies found in East Indonesia (Cox et al., 2010). A study suggesting that East Indonesian, including Papuan ancestor, was descended from pre-Austronesian activity that started to migrate across eastern Indonesia, was mixed with occupant groups of Papuans from west to east around 4,000 years ago (Xu et al., 2012).


In the present study, the frequencies of the allele of CYP2C9*2 and CYP2C19*17 was 0%, while CYP2C9*3 was 17%. Moreover, in the previous study of Buginese ethnic in Indonesia, the frequencies allele of CYP2C9*2 was absent, CYP2C9*3, CYP2C19*17 was 1.56, and 4.68%, respectively (Ikawati et al., 2014). According to the previous studies, the allele frequency of CYP2C9*2 in European, Caucasian, Japan, Jahai (Malay) were 10, 7, 28, 0%, respectively. The frequencies of CYP2C9*3 in Asian, European, Caucasian, Chinese, Japan, Jahai (Malay) were 6, 5.8, 7, 4, 2.7, 36.2% &, respectively (; (Allabi et al., 2003; Kimura et al., 1998; Ota et al., 2015; Rosdi
et al., 2016; Sugimoto et al., 2008).  And the values for CYP2C19*17 in Caucasian, Chinese, Japan, and Macedonian were 18, 3, 1, and 20.1% (Allabi et al., 2003; Sugimoto et al., 2008; Zhou et al., 2010; Jakjovski et al., 2014; Ota et al., 2015).


Negritos studies in Malaysia ranked CYP2C9*3 allele prevalence at 36.2 percent (Rosdi et al., 2016). The study argues that its proportion was the highest percentage of polymorphism in Malaysia regions while the Buginese population was absent (Indonesia's South Sulawesi) (Ikawati et al., 2014).


Besides, the lowest frequent polymorphism of CYP2C9*3 was found in Papuan subjects at 17 percent. The statistical representation of the CYP2C9*2 and CYP2C19*17 alleles frequencies in this subject was null. The Pearson x2 test was applied, examining differences among Buginese samples of the CYP2C9 allele, and showing no significant differences.



To the high enrichment our knowledge, this is the first study to show on CYP2C9 (CYP2C9*2, CYP2C9*3) and CYP2C19 (CYP2C19*17) genotype and allele frequency in the Negrito tribe in Indonesia, in recording and exploring information related to gene polymorphism, this research offers a valuable database. The finding might also be valuable for the clinicians to determine a new diagnostic approach and clinical setting. The absence of frequency polymorphism distribution in the Papuan population may indicate that indigenous Papuans are not from the Asia region, this is in line with previous study and 1000 Genomes Browser data that the citizens of South Asia have around 3% and 15-20% of specific frequencies of allelic CYP2C9*2 and CYP2C19*17 (Hill et al., 2007), while Papuan population revealed the contradiction result which was an absence of the alleles from in this study. 



We thank Professor Zullies Ikawati as a supervisor, Professor Mustofa, Hamim Sadewa, Ph.D., and Dr.rer.nat.Adam Hemawan for their helpful guidance.  


The authors report no conflicts of interest in this work.



Allabi, A.C., Gala, J., Desager, J., Heusterspreute, M., and Horsmans, Y. 2003. Genetic polymorphisms of CYP2C9 and CYP2C19 in the Beninese and Belgian populations. 653–657.


Bachtiar, M., Ooi, B.N.S., Wang, J., Jin, Y., Tan, T.W., Chong, S.S., and Lee, C.G.L. 2019. Towards precision medicine: interrogating the human genome to identify drug pathways associated with potentially functional, population-differentiated polymorphisms. Pharmacogenomics Journal. 19: 516–527.


Chisholm, B. 1995. The History and Geography of Human Genes. By L. Luca Cavalli-Sforza Paolo Menozzi and Alberto Piazza. Princeton, New Jersey: Princeton University Press, 1994. xiii, 526 maps, 541 pp. text. $150.00. The Journal of Asian Studies. 54: 490–492.


Cox, M.P., Karafet, T.M., Lansing, J.S., Sudoyo, H., and Hammer, M.F. 2010. Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian-Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates. Proceedings. Biological Sciences. 277: 1589–1596.


Gawroñska-Szklarz, B., Adamiak-Giera, U., Wyska, E., Kurzawski, M., Gornik, W., Kaldonska, M., and Drozdzik, M. 2012. CYP2C19 polymorphism affects single-dose pharmacokinetics of oral pantoprazole in healthy volunteers. European Journal of Clinical Pharmacology. 68: 1267–1274.


Hill, C., Soares, P., Mormina, M., Macaulay, V., Clarke, D., Blumbach, P.B., Vizuete-Forster, M., Forster, P., Bulbeck, D., Oppenheimer, S., and Richards, M. 2007. A mitochondrial stratigraphy for island southeast Asia. American Journal of Human Genetics. 80: 29–43.


Hirota, T., Eguchi, S., and Ieiri, I. 2013. Impact of Genetic Polymorphisms in CYP2C9 and CYP2C19 on the Pharmacokinetics of Clinically Used Drugs. Drug Metabolism and Pharmacokinetics.


Ikawati, Z., D Askitosari, T., Hakim, L., Tucci, J., and Mitchell, J., 2014. Allele frequency distributions of the drug metabolizer genes CYP2C9*2, CYP2C9*3, and CYP2C19*17 in the Buginese population of Indonesia. Current Pharmacogenomics and Personalized Medicine (Formerly Current Pharmacogenomics). 12: 236-239.


Jakjovski, K., Labachevski, N., Petlichkovski, A., Senev, A., Trojacanec, J., Atanasovska, E., Kostova, E., and Spiroski, M. 2014. Distribution of CYP2C9 and VKORC1 gene polymorphisms in healthy Macedonian male population. Macedonian Journal of Medical Sciences. 6: 339–343.


Kimura, M., Ieiri, I., Mamiya, K., Urae, A., and Higuchi, S. 1998. Genetic Polymorphism of Cytochrome P450s, CYP2C19, and CYP2C9 in a Japanese Population. Therapeutic Drug Monitoring, 20(3).,_CYP2C19,.1.aspx


Lazar, A., Tomalik-Scharte, D., and Fuhr, U. 2004. Chapter 13 - Applications of genotyping and phenotyping for clinically relevant polymorphisms of drug metabolizing enzymes and drug transporters. In G. Hempel (Ed.), Handbook of Analytical Separations. Elsevier Science B.V. 5: 321–353.


Li-wan-po, A., Girard, T., Farndon, P., Cooley, C., and Lithgow, J. 2010. Pharmacogenetics of CYP2C19 : functional and clinical implications of a new variant CYP2C19 *. 17.


Mcgraw, J. and Waller, D. 2012. Cytochrome P450 variations in different ethnic populations. February 2015.


Ota, T., Kamada, Y., Hayashida, M., Iwao-Koizumi, K., Murata, S., and Kinoshita, K. 2015. Combination analysis in genetic polymorphisms of drug-metabolizing enzymes CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A5 in the Japanese population. International Journal of Medical Sciences. 12: 78–82.


Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, M.R., Pugach, I., Ko, A.M. S., Ko, Y.C., Jinam, T.A., Phipps, M.E., Saitou, N., Wollstein, A., Kayser, M., Pääbo, S., and Stoneking, M. 2011. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. American Journal of Human Genetics. 89: 516–528.


Rendic, S. and Guengerich, F.P. (n.d.). Update Information on Drug Metabolism Systems-2009, Part ii: summary of information on the effects of diseases and environmental factors on human cytochrome p450 (CYP) enzymes and transporters.


Rettie, A.E. and Jones, J.P. 2005. Clinical and toxicological relevance of CYP2C9: Drug-drug interactions and pharmacogenetics. In Annual Review of Pharmacology and Toxicology. 45: 477–494.


Rodriguez, S., Gaunt, T.R., and Day, I.N.M. 2009. Hardy-Weinberg equilibrium testing of biological ascertainment for Mendelian randomization studies. American Journal of Epidemiology. 169: 505–514.


Romkes, M., Faletto, M.B., Blaisdell, J.A., Raucy, J.L., and Goldstein, J.A. 1993. Cloning and expression of complementary DNAs for multiple members of the human cytochrome P450IIC subfamily. [Erratum to document cited in CA114(15):137136r]. Biochemistry. 32: 1390.


Rosdi, R.A., Mohd Yusoff, N., Ismail, R., Soo Choon, T., Saleem, M., Musa, N., and Yusoff, S. 2016. High allele frequency of CYP2C9*3 (rs1057910) in a Negrito’s subtribe population in Malaysia; Aboriginal people of Jahai. Annals of Human Biology. 43: 445–450.


Rosemary, J. and Adithan, C. 2007. The Pharmacogenetics of CYP2C9 and CYP2C19: Ethnic Variation and Clinical Significance. In Current Clinical Pharmacology. 2.


Saberi, M., Ramazani, Z., Rashidi, H., and Saberi, A. 2020. The effect of CYP2C9 genotype variants in type 2 diabetes on the pharmacological effectiveness of sulfonylureas, diabetic retinopathy, and nephropathy. Vascular Health and Risk Management. 16:241–248.


Scordo, M. G., Aklillu, E., Yasar, U., Dahl, M., and Spina, E. 2001. Genetic polymorphism of cytochrome P450 2C9 in a Caucasian and a black African population. 447–450.


Soares, P., Trejaut, J.A., Loo, J.-H., Hill, C., Mormina, M., Lee, C.-L., Chen, Y.-M., Hudjashov, G., Forster, P., Macaulay, V., et al. 2008. Climate change and postglacial human dispersals in southeast Asia. Molecular Biology and Evolution, 25: 1209–1218.


Sugimoto, K., Uno, T., Yamazaki, H., and Tateishi, T. 2008. Limited frequency of the CYP2C19*17 allele and its minor role in a Japanese population. British Journal of Clinical Pharmacology. 65: 437–439.


Wollstein, A., Lao, O., Becker, C., Brauer, S., Trent, R.J., Nürnberg, P., Stoneking, M., and Kayser, M. 2010. Demographic history of oceania inferred from genome-wide data. Current Biology. 20: 1983–1992.


Xie, H.-G., Prasad, H.C., Kim, R.B., and Stein, C.M. 2002. CYP2C9 allelic variants: ethnic distribution and functional significance. Advanced Drug Delivery Reviews. 54: 1257–1270.


Xu, S., Pugach, I., Stoneking, M., Kayser, M., and Jin, L. 2012. Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion. Proceedings of the National Academy of Sciences of the United States of America. 109: 4574–4579.


Zanger, U.M. and Klein, K. 2013. Pharmacogenetics of cytochrome P450 2B6 (CYP2B6): Advances on polymorphisms, mechanisms, and clinical relevance. In Frontiers in Genetics (Vol. 4, Issue MAR).


Zhou, S., Zhou, Z., and Huang, M. 2010. Polymorphisms of human cytochrome P450 2C9 and the functional relevance. Toxicology. 278: 165–188.


OPEN access freely available online

Chiang Mai University Journal of Natural Sciences [ISSN 16851994]

Chiang Mai University, Thailand

Syahrul Tuba1,*, Zullies Ikawati2, and Mustofa3 

1 Faculty of Military Pharmacy, Department of Pharmacy, Indonesia Defense University, Sentul, Bogor, 16810, Indonesia.

2 Faculty of Pharmacy, Department of Clinical Pharmacy, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia

3 Faculty of Medicine, Department of Pharmacology Molecular, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia


Corresponding author: Syahrul Tuba, E-mail:

Total Article Views

Editor: Korakot Nganvongpanit, Chiang Mai University, Thailand


Article history:

Received: November 10, 2020;

Revised: February 19, 2021;

Accepted: April 4, 2021;

Published online: May 18, 2021