| Objective To investigate whether the Polymorphic of chloride channel gene CLCN2 which encoding voltage-gated chloride ion channel CLC-2 is associated with idiopathic generalized epilepsy syndrome(IGEs)of five unique minority and Han people in Yunnan Province.Methods Six single-nucleotide polymorphisms in CLCN2 gene of 92 patients with IGEs and 170 their relatives without disease from five unique minority (Jinuo people, Achang people, Bulang people, Wa people, Lahu people),107 IGEs patients and 63 normal controls of Han people fromYunnan, were selected to conduct sequence analysis through PCR,SNap shot sequencing and case-control study to detect association between gene polymorphism and idiopathic generalized epilepsies syndrome of these six people in Yunnan Province.Results Genotype frequency of rs13099401 of CLCN2 gene between Minority patients with IGEs and the Han ethnic group and the Han case group were significantly different(x2=6.828, p=0.033; x2=9.246,p=0.010. p<0.05); genotype CC and non-CC type in the case group of minority and the control group of Han people has a statistically significant difference (x2=9.245,p=0.002,OR=3.26, p<0.01).The genotype frequencies of rs2228291 between the minority patient group and the case group of Han people,and the control group of Han people were different in the distribution (x2=6.996, p=0.030; x2=8.058, p=0.018, p<0.05),There was statistically significant difference between the ethnic controls,the Han people with IGEs and the Han controls (x2=13.449, P=0.001;χ2=19.382, P=0.000, p<0.01); the distribution of genotype CT and non-CT, genotype TT and non-TT in the control group of minority and the case group of the Han people was statistically difference (χ2=16.793, p=0.000, OR=0.357;χ2=17.478, p=0.000, OR=3.034, p<0.01).The frequency of cases in minority ethnic group and the control group, the Han group with IGEs and the normal control had no significant differences in rs4912540, rs6770808 locus(p>0.05). There was a significant difference in genotype frequencies of rs9820367 locus between the minority patient group and the control group of Han people,the ethnic controls group and the Han control group (x2=11.032, p=0.003; x2=13.888, p=0.001, p<0.01),we do not find genotype CC in the case group of Han people. Genetype CG and non-CG,GG and non-GG in the ethnic case and the Han patients,in the ethnic controls group and the Han control,in the ethnic controls group and the Han patients have significant difference (p<0.01), there is statistically difference in GG and non-GG genotype between the control and the case of the Han people (χ2=6.755, p=0.014, OR=0.152,p<0.05).rs6773786 were statistically different between the Han ethnic group and the minorities case,the Han ethnic group and the minorities. (χ2=8.958, p= 0.011, p<0.05;χ2=9.375, p=0.009, p<0.01); genotype CG and non CG in the Han ethnic group and the control of minority had a significant statistical difference (x2=9.370, p=0.002, OR=2.682, p<0.01).Conclusion This study shows that the SNP at rs 13099401 in CLCN2 gene is associated with primary generalized epilepsy syndrome (IGEs) in the minority of yunnan.genotype CC play a protect role in the IGEs patient of Han people; Gene polymorphism in rs2228291 has relevant to the Han people with IGEs, which has ethnic differences in genotype frequency distributions, the genotypes CT may increase the risk of IGEs in Han people, and TT genotype may be the protective factors of the minority patient with IGEs; There no significant correlation between site rs4912540 and rs6770808 in Yunnan people; Gene polymorphism in rs9820367 is associated with the Han people with IGEs, which has ethnic differences in genotype frequency distributions, there no genotype CC in the case group of Han people, genotype CC may be a protective factors, however, the GG type increase the risk in the patients; The SNP of rs6773786 is related to IGEs in Han people, CG genotypes increased the risk of illness.
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