一个孤独症谱系障碍核心家系KIF1A基因错义变异及其蛋白表达和结构分析

A study on KIF1A gene missense variant analysis and its protein expression and structure profiles of an autism spectrum disorder family trio

目的报告1个携带KIF1A基因错义变异的孤独症谱系障碍核心家系,并分析KIF1A基因的致病变异及其表达蛋白结构。方法提取患儿及其双亲外周血DNA,利用全外显子组测序(whole exome sequencing,WES)技术进行测序,并应用Sanger测序法进行验证。对可疑变异分别用SIFT、PolyPhen-2、Mutation Taster和CADD生物信息学软件分析变异的有害性和保守性;用人脑转录组学(human brain transcriptome,HBT)数据库分析KIF1A基因在脑内的表达情况;进一步分别用PredictProtein和SWISS-MODEL来预测KIF1A野生型蛋白和变异型蛋白的二级结构和三级结构;用PyMOL V2.4来考察蛋白变异后氢键连接的改变。结果WES测序结果显示患儿KIF1A基因存在c.664A>C(p.Asn222His)错义变异,且该变异在中国人群中未见报道。有害性预测结果均提示该变异为有害变异。分析该基因在脑内的表达水平,发现其在胚胎发育阶段、各脑区均广泛表达。分析变异后的蛋白结构,发现该错义变异会导致蛋白二级结构中的α螺旋、β折叠和蛋白结合域等结构的诸多改变,氢键连接及空间结构也会发生改变,从而使原有的生物学功能改变。结论KIF1A基因可能是孤独症谱系障碍的风险基因。

Objective To analyze the pathogenic variants of the KIF1A gene and its corresponding protein structure in an autism spectrum disorder(ASD)family trio carrying harmful missense variants in the KIF1A gene.Methods The peripheral blood DNA of the patient and his parents was extracted and sequenced using whole exome sequencing(WES)technology and verified by Sanger sequencing.Bioinformatics software SIFT,PolyPhen-2,Mutation Taster,and CADD software were used to analyze the harmfulness and conservation of variants.The Human Brain Transcriptome(HBT)database was used to analyze the expression of the KIF1A gene in the brain.PredictProtein and SWISS-MODEL were further used to predict the secondary structure and tertiary structure of KIF1A wild-type protein and variant protein.PyMOL V2.4 was utilized to investigate the change of hydrogen bond connection after protein variant.Results The WES sequencing revealed a missense variant c.664A>C(p.Asn222His)in the child’s KIF1A gene,and this variant was a de novo variant.The harmfulness prediction results suggest that this variant is harmful.By analyzing expression level of KIF1A gene in the brain.It is found that KIF1A gene widely expressed in various brain regions during embryonic development.By analyzing the variant protein structure,the missense variant of KIF1A will cause many changes in the secondary structure of protein,such asα-helix,β-strand,and protein binding domain.The connection of hydrogen bond and spatial structure will also change,thereby changing the original biological function.Conclusion The KIF1A gene may be a risk gene for ASD.