Genetic analysis of a Chinese pedigree with Cohen syndrome due to compound heterozygous variants ofVPS13B gene
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目的 分析1个Cohen综合征家系的临床表型与遗传学特征，并为产前诊断提供实验依据。 方法 选取2021年6月2日因"智力障碍及发育迟缓"就诊于郑州人民医院的Cohen综合征女性先证者、先证者妹妹及其家系成员(3代共11人)作为研究对象，收集先证者及先证者妹妹的临床资料。提取该家系成员外周血样品及胎儿胎盘绒毛样品基因组DNA，利用染色体微阵列技术(CMA)检测先证者染色体异常情况。利用全外显子组测序(WES)及Sanger测序，寻找先证者候选变异位点，并进行家系验证。提取家系成员外周血RNA，进行体内剪接变异体检测，应用RT-PCR分析VPS13B基因的mRNA表达水平，并对胎龄12周的胎儿的进行产前诊断。 结果 先证者为10岁女性，临床表现为发育迟缓、躯体肥胖、高度近视、特殊面容。先证者妹妹为3岁女性，具有与先证者相同表型。CMA结果提示先证者染色体未见异常。WES结果发现先证者及其妹妹VPS13B基因存在2个杂合变异，分别为c.10076_10077delCA(p.T3359fs*29)缺失移码变异及c.6940+1G>T剪接位点变异，均已有报道。母亲为c.10076_10077delCA(p.T3359fs*29)变异携带者，遗传自先证者外祖父。父亲为c.6940+1G>T变异携带者，遗传自先证者祖母。根据美国医学遗传学与基因组学学会遗传变异分类标准与指南，c.10076_10077delCA评级为致病性变异(PVS1+PS4+PM4+PP1)，c.6940+1G>T评级为致病性变异(PVS1+PM2_Supporting+PM3+PP1)。c.6940+1G>T剪接位点变异导致VPS13B基因第38外显子发生跳跃，产生1个缺失69个氨基酸的转录本。与对照组相比，先证者父母在外周血中mRNA表达水平降低至65%~70%(P<0.01)、先证者及其妹妹降低至40%(P<0.001)。对胎龄12周的胎儿的产前诊断发现胎儿存在c.10076_10077delCA杂合变异。 结论 VPS13B基因的c.10076_10077delCA(p.T3359fs*29)缺失移码变异及c.6940+1G>T剪接位点变异考虑为该家系先证者及其妹妹患Cohen综合征的致病原因。基因检测技术可以辅助临床医师诊断Cohen综合征。 Objective To investigate the clinical phenotype and genetic characteristics of a Chinese pedigree affected with Cohen syndrome. Methods A proband who was admitted to Zhengzhou People′s Hospital on June 2, 2021 due to intellectual disability and developmental delay, in addition with her younger sister and other family members, were selected as the study subjects. The clinical data of the proband and her younger sister were collected. Genomic DNA was extracted from peripheral venous blood and chorionic villi samples. Chromosomal abnormalities were detected with chromosomal microarray analysis (CMA). Whole exome sequencing (WES) and Sanger sequencing were carried out to detect candidate variants in the proband. With RNA extracted from the peripheral blood samples VPS13B gene transcripts and expression were analyzed by PCR and real-time quantitative PCR. Prenatal diagnosis was carried out at 12 weeks′ gestation. Results The proband was a 10-year-old female with clinical manifestations including development delay, obesity, severe myopia and peculiar facial features. Her sister was 3 years old with a similar phenotype. CMA revealed no chromosomal abnormality in the proband, while WES results revealed that the proband and her sister had both harbored compound heterozygous variants of the VPS13B gene, namely c. 10076_10077delCA (p.T3359fs*29) and c. 6940+ 1G>T, which were respectively inherited from their mother and father. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), both variants were classified as pathogenic (PVS1+ PS4+ PM4+ PP1 PVS1+ PM2_Supporting+ PM3+ PP1).In vivo splicing assay confirmed that the c. 6940+ 1G>T variant has produced a frameshift transcript with skipping of exon 38. Compared with the control group, the expression of RNA in the peripheral blood of the proband′s parents has decreased to 65%~70% (P< 0.01), whilst that in the proband and her sister has decreased to 40% (P < 0.001). Prenatal diagnosis at 12 weeks of gestation has found that the fetus only harbored the heterozygous c. 10076_ 10077delCA variant. Conclusion The c. 10076_10077delCA (p.T3359fs*29) frameshift variant and c. 6940+ 1G>T splicing variant probably underlay the Cohen syndrome in this pedigree. Genetic testing has facilitated the diagnosis of this disease.
Objective To investigate the clinical phenotype and genetic characteristics of a Chinese pedigree affected with Cohen syndrome. Methods A proband who was admitted to Zhengzhou People′s Hospital on June 2, 2021 due to intellectual disability and developmental delay, in addition with her younger sister and other family members, were selected as the study subjects. The clinical data of the proband and her younger sister were collected. Genomic DNA was extracted from peripheral venous blood and chorionic villi samples. Chromosomal abnormalities were detected with chromosomal microarray analysis (CMA). Whole exome sequencing (WES) and Sanger sequencing were carried out to detect candidate variants in the proband. With RNA extracted from the peripheral blood samples VPS13B gene transcripts and expression were analyzed by PCR and real-time quantitative PCR. Prenatal diagnosis was carried out at 12 weeks′ gestation. Results The proband was a 10-year-old female with clinical manifestations including development delay, obesity, severe myopia and peculiar facial features. Her sister was 3 years old with a similar phenotype. CMA revealed no chromosomal abnormality in the proband, while WES results revealed that the proband and her sister had both harbored compound heterozygous variants of the VPS13B gene, namely c. 10076_10077delCA (p.T3359fs*29) and c. 6940+ 1G>T, which were respectively inherited from their mother and father. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), both variants were classified as pathogenic (PVS1+ PS4+ PM4+ PP1 PVS1+ PM2_Supporting+ PM3+ PP1).In vivo splicing assay confirmed that the c. 6940+ 1G>T variant has produced a frameshift transcript with skipping of exon 38. Compared with the control group, the expression of RNA in the peripheral blood of the proband′s parents has decreased to 65%~70% (P< 0.01), whilst that in the proband and her sister has decreased to 40% (P < 0.001). Prenatal diagnosis at 12 weeks of gestation has found that the fetus only harbored the heterozygous c. 10076_ 10077delCA variant. Conclusion The c. 10076_10077delCA (p.T3359fs*29) frameshift variant and c. 6940+ 1G>T splicing variant probably underlay the Cohen syndrome in this pedigree. Genetic testing has facilitated the diagnosis of this disease.
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