OBJECTIVE:To explore the genetic etiology of a pedigree with intellectual disability and explore its pathogenesis. METHODS:A Chinese pedigree which had presented at the Henan Provincial People's Hospital in March 2023 was selected as the study subject. Clinical data of the pedigree were collected, along with peripheral venous blood samples from its members. Whole exome sequencing (WES) was carried out, and candidate variants were verified by Sanger sequencing. Amniotic fluid was collected for prenatal diagnosis. This study was approved by the Medical Ethics Committee of the Henan Provincial People's Hospital (Ethics No. 2019-134). RESULTS:Both the proband (a 6-year-old male) and his mother (30 years old) had various degrees of intellectual and motor impairment. WES revealed that the proband has harbored a de novo heterozygous c.2563_2567dup (p.Lys856fs) variant of the UBE3A gene, while his mother, maternal grandmother and fetus had all harbored a novel heterozygous c.409+1G>A variant of the RNF13 gene. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), both variants were predicted to be pathogenic (PVS1+PS1+PM2_Supporting; PVS1+PM2_Supporting+PP3). CONCLUSION:Based on the clinical manifestations and the result of genetic testing, the heterozygous c.2563_2567dup (p.Lys856fs) variant of the UBE3A gene probably underlay the intellectual disability and developmental delay in the proband, whilst the heterozygous c.409+1G>A variant of the RNF13 gene may underlie the intellectual disability in the proband's mother and grandmother. Above results have enabled genetic counseling and prenatal diagnosis for this pedigree.

OBJECTIVE:To explore the value of whole exome sequencing for the inferential analysis of recessive genetic disease carrier status for couples with a child died of Primary immunodeficiency (PID).METHODS:Clinical data was collected from four couples with a childbearing history of PID who had sought genetic counseling and undergone genetic testing at Henan Provincial People's Hospital from February 2017 to December 2021. Whole exome sequencing (WES) was performed on both partners of each couple, and candidate variants were validated by Sanger sequencing and fluorescent quantitative PCR. Prenatal diagnosis was conducted on fetuses of these couples after confirming the variants.RESULTS:A total of six variants were detected in four genes including IL2RG, BTK, CYBB, and DUOX2. Among these, the c.1265G>A and c.3329G>A variants of the DUOX2 gene and the c.676C>T variant of the IL2RG gene were previously known as pathogenic variants. On the other hand, the Exon5_8del variant of the IL2RG gene, the c.184_185delAC variant of the BTK gene, and the c.472A>T variant of the CYBB gene were unreported previously. Based on the guidelines from the American College of Medical Genetics and Genomics, the IL2RG: Exon5_8del, BTK: c.184_185delAC and CYBB: c.472A>T variants were classified as likely pathogenic (PVS1+PM2_Supporting+PP4).Prenatal diagnosis was conducted for three couples during their subsequent pregnancies, and the results revealed that the fetuses had the wild-type genotypes at the c.184_185 position of the BTK gene, the c.472 position of the CYBB gene, and the c.676 position of the IL2RG gene. Follow-up examinations one year after birth has found no abnormality in the infants.CONCLUSION:WES is an important tool to infer and analyze the carrier status for couples who had given births to children died of PID and improve the positive detection rate.

OBJECTIVE:To explore the genetic etiology of two patients with developmental delay and intellectual disability.METHODS:Two children who were respectively admitted to Henan Provincial People's Hospital on August 29, 2021 and August 5, 2019 were selected as the study subjects. Clinical data were collected, and array comparative genomic hybridization (aCGH) was carried out on the children and their parents for the detection of chromosomal microduplication/microdeletions.RESULTS:Patient 1 was a 2-year-and-10-month female and patient 2 was a 3-year-old female. Both children had featured developmental delay, intellectual disability, and abnormal findings on cranial MRI. aCGH revealed that patient 1 has harbored arr[hg19] 6q14.2q15(84621837_90815662)×1, a 6.19 Mb deletion at 6q14.2q15, which encompassed ZNF292, the pathogenic gene for Autosomal dominant intellectual developmental disorder 64. Patient 2 has harbored arr[hg19] 22q13.31q13.33(46294326_51178264)×1, a 4.88 Mb deletion at 22q13.31q13.33 encompassing the SHANK3 gene, haploinsufficiency of which can lead to Phelan-McDermid syndrome. Both deletions were classified as pathogenic CNVs based on the guidelines of American College of Medical Genetics and Genomics (ACMG) and were not found in their parents.CONCLUSION:The 6q14.2q15 deletion and 22q13-31q13.33 deletion probably underlay the developmental delay and intellectual disability in the two children, respectively. Haploinsufficiency of the ZNF292 gene may account for the key clinical features of the 6q14.2q15 deletion.

目的 分析两个营养不良型大疱性表皮松解症家系的临床特点和致病基因,揭示疾病的发生机制和患者表型差异机制.方法 从两家系成员的外周血中提取DNA进行高通量测序及Sanger测序验证.结果 临床资料分析显示,2个家系先证者的临床表现符合营养不良型大疱性表皮松解症的诊断,其中家系1先证者症状明显重于家系中其他患者.基因测序结果显示,家系1患者均携带COL7A1基因c.6082G＞C(p.G2028R)突变,同时先证者及其表型正常的母亲和舅舅还携带该基因致病性剪切位点突变c.7068+2(IVS91)T＞G,为首次报道致病突变.家系2先证者携带COL7A1基因c.6081_6082insC(p.G2028Rfs*71)突变和首次报道的c.1892G＞A(p.W631X)突变,分别来自其父母.结论 家系1先证者同时携带2个致病突变可能是其严重临床表型的分子机制;首次报道的COL7A1基因突变丰富了该基因突变谱.

OBJECTIVE To explore the clinical characteristics and genetic basis of two Chinese pedigrees affected with Joubert syndrome. METHODS Clinical data of the two pedigrees was collected. Genomic DNA was extracted from peripheral blood samples and subjected to high-throughput sequencing. Candidate variants were verified by Sanger sequencing. Prenatal diagnosis was carried out for a high-risk fetus from pedigree 2. RESULTS The proband of pedigree 1 was a fetus at 23+5 weeks gestation, for which both ultrasound and MRI showed "cerebellar vermis malformation" and "molar tooth sign". No apparent abnormality was noted in the fetus after elected abortion. The fetus was found to harbor c.812+3G>T and c.1828G>C compound heterozygous variants of the INPP5E gene, which have been associated with Joubert syndrome type 1. The proband from pedigree 2 had growth retardation, mental deficiency, peculiar facial features, low muscle tone and postaxial polydactyly of right foot. MRI also revealed "cerebellar dysplasia" and "molar tooth sign". The proband was found to harbor c.485C>G and c.1878+1G>A compound heterozygous variants of the ARMC9 gene, which have been associated with Joubert syndrome type 30. Prenatal diagnosis found that the fetus only carried the c.485C>G variant. A healthy infant was born, and no anomalies was found during the follow-up. CONCLUSION The compound heterozygous variants of the INPP5E and ARMC9 genes probably underlay the disease in the two pedigrees. Above finding has expanded the spectrum of pathogenic variants underlying Joubert syndrome and provided a basis for genetic counseling and prenatal diagnosis.

Objective:To explore the genetic basis for fetus with bilateral lateral ventriculomegaly.Methods:Fetus umbilical cord blood and peripheral blood samples of its parents were collected. The fetus was subjected to chromosomal karyotyping, whilst the fetus and its parents were subjected to array comparative genomic hybridization (aCGH). The candidate copy number variation (CNV) were verified by qPCR, Application goldeneye DNA identification system was used to confirm the parental relationship.Results:The fetus was found to have a normal karyotype. aCGH analysis indicated that it has carried a 1.16 Mb deletion at 17p13.3, which partially overlapped with the critical region of Miller-Dieker syndrome (MDS), in addition with a 1.33 Mb deletion at 17p12 region, which is associated with hereditary stress-susceptible peripheral neuropathy (HNPP). Its mother was also found to harbor the 1.33 Mb deletion at 17p12. qPCR analysis confirmed that the expression levels of genes from the 17p13.3 and 17p12 regions were about the half of that in the normal control, as well as the maternal peripheral blood sample. Parental relationship was confirmed between the fetus and its parents. Following genetic counseling, the parents has chosen to continue with the pregnancy.Conclusion:The fetus was diagnosed with Miller-Dieker syndrome due to the de novo deletion at 17p13.3. Ventriculomegaly may be an important indicator for prenatal ultrasonography in fetuses with MDS.

OBJECTIVE To explore the clinical features and genetic etiology of two children with intellectual developmental disorder and microcephaly with pontine and cerebellar hypoplasia (MICPCH). METHODS Two children with MICPCH who were presented at the Henan Provincial People's Hospital between April 2019 and December 2021 were selected as the study subjects. Clinical data of the two children were collected, along with peripheral venous blood samples of them and their parents, and amniotic fluid sample of the mother of child 1. Whole exome sequencing (WES), array-comparative genomic hybridization (aCGH) and real-time quantitative PCR (qPCR) were carried out for the children, their parents and the fetus. The pathogenicity of candidate variants were evaluated. RESULTS Child 1 was a 6-year-old girl featuring motor and language delay, whilst child 2 was a 4.5-year-old girl mainly featuring microcephaly and mental retardation. WES revealed that child 2 has harbored a 158.7 kb duplication in Xp11.4 (chrX: 41446160_41604854), which has encompassed exons 4~14 of the CASK gene. The same duplication was not found in either of her parents. aCGH revealed that child 1 has harbored a 29 kb deletion at Xp11.4 (chrX: 41637892_41666665), which encompassed exon 3 of the CASK gene. The same deletion was not found in either of her parents and the fetus. The above results were confirmed by qPCR assay. Above deletion and duplication were not found in the ExAC, 1000 Genomes and gnomAD databases. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), both variants were rated as likely pathogenic (PS2+PM2_Supporting). CONCLUSION The deletion of exon 3 and duplication of exons 4~14 of the CASK gene probably underlay the pathogenesis of MICPCH in these two children, respectively.

OBJECTIVE:To analyze the clinical features and genetic variant in a patient with Usher syndrome.METHODS:Whole exome sequencing was carried out for the patient. Suspected variants were validated by Sanger sequencing of her parents and fetus.RESULTS:The proband was found to harbor compound heterozygous variants c.17_18insA (p.Tyr6Ter*) and c.4095_4096insA (p.Arg1366Lys fs*38) of the PCDH15 gene (NM_033056), which were respectively inherited from her father and mother. The same variants were not detected in 100 healthy controls. Based on the guidelines of the American Society of Medical Genetics and Genomics, both variants were predicted to be pathogenic (PVS1+PM2+PP4). By prenatal diagnosis, her fetus was found to carry the c.4095_4096insA variant. After birth, the child has passed neonatal hearing screening test, and no abnormal auditory and visual function was found after the first year.CONCLUSION:The compound heterozygous variants c.17_18insA (p.Tyr6Ter*) and c.4095_4096insA (p.Arg1366Lys fs*38) of the PCDH15 gene probably underlay the Usher syndrome is this proband.

目的 分析1个发育性癫痫性脑病75型(developmental and epileptic encephalopathy 75,DEE75)家系3例患儿的临床特征,探讨该家系线粒体脯氨酰tRNA合成酶2(prolyl-tRNA synthetase 2,mitochondrial,PARS2)基因突变情况.方法 分析该DEE75家系3例患儿(先证者及其哥哥、弟弟)的临床资料;对先证者及其父母进行全外显子组测序,对鉴定出的可疑致病突变在先证者及其弟弟、父母中采用Sanger测序法进行验证;对未报道的可疑致病突变进行生物信息学分析、蛋白质结构模型预测.结果 该家系3例患儿均存在小头畸形、发育迟缓、智力障碍等表型,先证者哥哥有癫痫表现.先证者及其弟弟均存在PARS2基因c.283G＞A(p.Val95Ile)、c.664A＞G(p.Thr222Ala)及c.1059A＞C(p.Glu353Asp)复合杂合错义突变,先证者母亲存在c.283G＞A错义突变,先证者父亲存在c.664A＞G及c.1059A＞C错义突变.生物信息学分析显示c.664A＞G及c.1059A＞C为未报道的可能有害突变.蛋白质结构预测显示c.664A＞G可能破坏蛋白质结构和功能而致病,c.1059A＞C对蛋白质结构无明显影响.结论 PARS2基因c.283G＞A及c.664A＞G复合杂合错义突变可能是该家系DEE75患儿的致病原因.

目的:对1个多发畸形胎儿的家系进行遗传学分析,为临床遗传咨询和产前诊断提供依据.方法:对1例孕中期发现胎儿多发畸形的孕妇进行产前三维系统超声检查;抽取羊水,进行染色体G显带核型分析和高通量测序;采集孕妇及其配偶的血样,应用Sanger测序技术验证基因的变异位点.结果:产前超声提示胎儿完全型心内膜垫缺损、胎儿多发畸形等.高通量测序结果显示胎儿的EVC2基因NM 147127:c.519+1G>C剪接位点杂合变异和EVC2基因NM 147127:c.903delG(p.phe302fs)缺失移码杂合变异;Sanger测序显示胎儿的母亲EVC2 基因NM 147127:c.519+1G>C剪接位点杂合变异,父亲EVC2基因NM 147127:c.903delG(p.phe302fs)缺失移码杂合变异;胎儿EVC2基因的两个变异分别源自其父母.结合遗传学分析和产前超声结果,该家系确诊为 Ellis-van Creveld综合征(EVC).结论:EVC2基因NM 147127:c.519+1G>C剪接位点杂合变异和EVC2基因NM 147127:c.903delG(p.phe302fs)缺失移码杂合变异可能为EVC的致病原因.

Objective:To explore the genetic etiology for a child featuring mental retardation and speech delay.Methods:Clinical data of the child was collected. DNA was extracted from peripheral blood samples of the child and members of his pedigree. Whole exome sequencing was carried out for the child, and candidate variants were verified by Sanger sequencing. Prenatal diagnosis was provided for his mother upon her subsequent pregnancy.Results:The child has mainly featured mental retardation, speech delay, ptosis, strabismus, photophobia, hyperactivity, and irritability. Whole exome sequencing revealed that he has harbored a pathogenic heterozygous variant of the KAT6A gene, namely c. 5314dupA (p.Ser1772fs*20), which was not detected in either of his parents. The child was diagnosed with Arboleda-Tham syndrome. The child was also found to harbor a hemizygous c. 56T>G (p.Leu19Trp) variant of the AIFM1 gene, for which his mother was heterozygous and his phenotypically normal maternal grandfather was hemizygous. Pathogenicity was excluded. Prenatal diagnosis has excluded the c. 5314dupA variant of the KAT6A gene in the fetus. Conclusion:The heterozygous c. 5314dupA (p.Ser1772fs*20) variant of the KAT6A gene probably underlay the Arboleda-Tham syndrome in this child. Above finding has enabled genetic counseling and prenatal diagnosis for this pedigree.

目的 分析脑肌酸缺乏综合征(cerebral creatine deficiency syndrome,CCDS)1型1家系的致病基因突变情况,并进行产前诊断.方法 采集先证者及其父母外周血提取基因组DNA,采用靶向捕获方法对基因组全部外显子区域进行测序,经比对分析发现可疑变异位点,采用Sanger测序法进行验证.明确致病变异后,采集母亲羊水,进行产前诊断并随访.结果 先证者存在SLC6A8基因(NM_005629)c.1631C＞T错义变异,该突变可导致其编码的544位脯氨酸被异亮氨酸代替;先证者母亲存在SLC6A8基因c.1631C＞T杂合变异;先证者父亲SLC6A8基因c.1631C＞T位点为野生型.Sanger测序显示,胎儿SLC6A8基因c.1631C＞T位点为野生型.出生后随访3个月,发育正常,未见CCDS 1型表型.结论 SLC6A8基因c.1631C＞T错义变异是该CCDS 1型家系的致病原因,基因诊断和产前诊断可有效降低生育CCDS 1型患儿的风险.

Objective:To analyze the pathogenic gene and prenatal diagnosis of a family with intellectual disability.Methods:Out of this family consisting of 17 members in three generations, four males had intellectual disability. The proband's elder sister (Ⅱ-7) visited Henan Provincial People's Hospital in Oct 2019 for genetic counseling at 8 weeks of gestation. After informed consent was obtained, peripheral blood samples of the family members were collected. The whole exome sequencing was performed on the genome DNA of the proband (Ⅱ-9, male) and his parents to screen the candidate variants for phenotype co-segregated analysis by Sanger sequencing. The expression vectors were constructed by homologous recombination and the splicing experiments were performed in vitro. Reverse transcription polymerase chain reaction, Sanger sequencing, and TA clone sequencing were used to analyze the effect of candidate variants on splicing. After the pathogenic variant was determined the proband's elder sister underwent prenatal diagnosis (Ⅲ-7) using goldeneyeTM20A genotyping system and Sanger sequencing. Results:A hemizygous synonymous variant of c.1302G>A (p. S434S) in DLG3 gene was found in the proband by whole exome sequencing, which was carried by his mother (Ⅰ-1) and co-segregated with the phenotype in other family patients. In vitro splicing experiment showed that c.1302G>A variant led to abnormal splicing of 88.24% transcripts, which further resulted in the reading frame shift and protein function impairment. The mutation was not detected in the fetus (Ⅲ-7), who was born alive later and showed no abnormal mental or behavioral development at the age of one and a half year and is still being followed up. Conclusions:The synonymous mutation c.1302G>A in DLG3 gene was the etiopathogenesis of X-linked intellectual disability in this family.

目的:分析一例产前超声提示先天性白内障胎儿的遗传学病因。方法:抽取孕妇羊水、孕妇及其丈夫的外周血样，对胎儿及其父母行家系全外显子组测序，对候选致病变异用Sanger测序法进行验证。结果:胎儿 GJA8基因(NM_005267)存在c.136G>C(p.Gly46Arg)错义杂合变异，其父母该位点均为野生型。 结论:GJA8基因(NM_005267)c.136G>C(p.Gly46Arg)错义杂合变异可能是胎儿罹患先天性白内障的原因。

Objective:To explore the genetic etiology of fetuses with high suspicion of congenital skeletal malformation detected by prenatal ultrasound.Methods:This retrospective study collected 21 pregnant women with highly suspected fetal skeletal malformation indicated by ultrasound (the couples had no skeletal malformation) at Institute of Medical Genetics, Henan Provincial People's Hospital from January 2019 to August 2020. Amniotic fluid/umbilical cord blood of the fetus and peripheral blood of the couples were obtained for karyotype analysis, chromosomal microarray analysis, and whole-exome sequencing. Sanger sequencing was performed for the "pathogenic" "suspected pathogenic" "variants of uncertain significance" variants detected by whole exome sequencing. Genetic etiology of the 21 fetuses was described.Results:A total of five chromosomal abnormalities were detected, including four cases of trisomy 21 and one trisomy 18. Chromosome microarray analysis detected one case of abnormal copy number variation, 16 p11.2 microdeletion syndrome. Ten cases of monogenic diseases were found by whole exome sequencing and eight genes were involved ( SGMS2, FGFR3, DYNC2H1, WDR35, TBX5, COL2A1, FGFR2, and ALPL). Totally, 14 variations were detected, among which seven were novel variations (c.8129T>A, c.7126G>A, c.10307_10320del, and c.2641G>T in DYNC2H1 gene; c.3085G>A and c.491G>A in WDR35 gene; c.1070G>T in COL2A1 gene). Conclusions:For fetus, whose parents have no skeletal malformation, highly suspected of congenital malformation of skeletal system by prenatal ultrasound, genetic factor is the primary reason, including chromosomal abnormalities, copy number variations, and monogenic mutations.