Clinical phenotype and genetic analysis of a fetus with a novel mutation of OTX2 gene

The use of fetal exome sequencing in prenatal diagnosis: a points to consider document of the American College of Medical Genetics and Genomics (ACMG)

ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG)

DNA-based screening and population health: a points to consider statement for programs and sponsoring organizations from the American College of Medical Genetics and Genomics (ACMG)

To explore the genetic etiology of a child with Brain small vessel disease 1 with ocular anomalies. A child who was admitted to Ningbo Women and Children's Hospital on May 28, 2022 was selected for the study. Clinical data were collected, and peripheral blood samples from the child and her parents were obtained for genomic DNA extraction. Whole exome sequencing (WES) was performed to screen for pathogenic variants. Candidate variants were validated via Sanger sequencing and subjected to bioinformatic analysis. This study was approved by the Medical Ethics Committee of Ningbo Women and Children's Hospital (Ethics No. EC2020-014). The child was a 7-year-old female with a diagnosis of epilepsy. WES revealed that she has carried a heterozygous missense variant in the COL4A1 gene: c.1792G>A (p.Gly598Ser). Sanger sequencing confirmed that her parents both had the wild-type genotype for this variant. Based on American College of Medical Genetics and Genomics (ACMG) Standards and Guidelines for the Interpretation of Sequence Variants, the variant were predicted to be a likely pathogenic (PS2+PM1+PM2_Supporting+PP3). Bioinformatics predicted that amino acid 598 was highly conserved in different species, formed hydrogen bond with Asp599 after becoming Ser598. The heterozygous missense variant of the COL4A1 gene c.1792T>C (p.G598S) could be the pathogenic cause of this child with Brain small vessel disease 1 with ocular anomalies.

To explore the genetic etiology and clinical phenotype of a child with Triadin knockout syndrome (TKOS), and to review the relevant literature of TKOS patients due to variants of TRDN gene. A child who was admitted to the Children's Hospital of Xi'an Jiaotong University on March 19, 2023 due to sudden cardiac arrest 3 days earlier was selected as the study subject. Peripheral blood samples (2 to 3 mL) were collected from the child and her parents for the extraction of genomic DNA and whole exome sequencing (WES). Pathogenic variants were searched from databases such as the Genome Aggregation Database (gnomAD) and Online Mendelian Inheritance in Man (OMIM), and were assessed based on the guidelines from the American College of Medical Genetics and Genomics (ACMG). Sanger sequencing was carried out for family validation of the pathogenic variants. Using keywords such as "arrhythmias" "TRDN" and "Triadin" both in Chinese and English, relevant literature on TKOS patients due to variants of the TRDN gene was retrieved from the CNKI, Wanfang Data Knowledge Service Platform, and PubMed databases, and the time of literature retrieval was set from January 1, 2012 to December 1, 2023. This study has been approved by the Ethics Committee of the Affiliated Children's Hospital of Xi'an Jiaotong University (No. 20230097), and informed consent was obtained from the parents of the child. The child had experienced syncope and cardiac arrest after exercise. Electrocardiographic examination revealed QTc interval prolongation, T-wave inversion in precordial leads V1-V3, polymorphic ventricular premature beat (VPB), and ventricular tachycardia (VT) along with increased heart rate. WES and Sanger sequencing revealed that the child has harbored a homozygous c.463del(p.E155Kfs*20) variant of the TRDN gene, for which both of the parents were heterozygous. Based on the guidelines from the ACMG, the variant was classified as pathogenic (PVS1+PM2+PM3). The child was ultimately diagnosed with TKOS. In total 12 publications on TOKS cases caused by TRDN gene variants were retrieved, which involved 30 patients and 28 carriers of single heterozygous variant of the TRDN gene. Among the 30 TKOS patients, 20 had carried homozygous variants of the TRDN gene, and 10 had carried compound heterozygous variants, and all had exhibited significant clinical phenotype of arrhythmia, with most cases had experienced malignant arrhythmia induced by exercise and/or excitement during infancy or early childhood, leading to recurrent syncope and cardiac arrest. Of note, none of the 28 carriers of single heterozygous variant had abnormal clinical phenotype. The homozygous c.463del(p.E155Kfs20) variant of the TRDN gene probably underlay the pathogenesis of cardiac arrest in this child. Above discovery has enriched the mutational spectrum of the TRDN gene.

The use of ACMG secondary findings recommendations for general population screening: a policy statement of the American College of Medical Genetics and Genomics (ACMG)

Updated recommendations for CFTR carrier screening: A position statement of the American College of Medical Genetics and Genomics (ACMG)

To explore the clinical phenotype and variants of KIF4A gene associated with X-linked intellectual disability type 100 (XLID100) in a child by whole-exome sequencing (WES). A child presented at the Children's Hospital Affiliated to Nanjing Medical University in September 2023 was selected as the study subject. Clinical data of the child was retrospectively analyzed. Peripheral blood samples were collected from the child and his family members for WES analysis. Candidate variant was verified by Sanger sequencing. Pathogenicity of the candidate variant was rated based on the guidelines from the American College of Medical Genetics and Genomics (ACMG). The variant was also searched in dbSNP, OMIM, HGMD, ClinVar and gnomAD databases. Amino acid sequences of the KIF4A protein across various species were retrieved from the Ensembl Genome Browser Database and analyzed using Clustal Omega software. Relevant literature on KIF4A gene mutations associated with XLID100 was reviewed. This study has been approved by the Medical Ethics Committee of the Hospital (Ethics No. 202402022-1). The child, a 3-year-6-month-old male, had manifested intellectual impairment, language delay, autism, and choroid cyst revealed by cranial magnetic resonance imaging. No facial dysmorphism, tooth anomaly, gross motor development delay or regression, and history of seizure and febrile convulsion was noted. WES revealed that he has harbored a c.3385delinsTATC (p.Thr1129delinsTyrPro) variant of the KIF4A gene. Sanger sequencing confirmed that his mother and sister have harbored the same variant, whilst his father was of the wild type. Both of his parents had a normal phenotype. The variant was classified as of uncertain significance based on the guidelines from the ACMG. It was not recorded by the dbSNP, OMIM, HGMD, ClinVar and the gnomAD database. Conservative analysis suggested that the variant site, which normally encodes a cysteine, is highly conserved among various species. A review of the literature had retrieved 6 relevant articles documenting a total of 27 cases of KIF4A gene mutations, with only one case from China. The c.3385delinsTATC (p.Thr1129delinsTyrPro) variant of the KIF4A gene probably underlay the XLID100 in this child. Above finding has provided a reference for the clinical diagnosis and genetic counseling and enriched the mutation spectrum of the KIF4A gene.

To explore the clinical characteristics and variant of FBP1 gene in a child with Fructose-1,6-bisphosphatase deficiency (FBP1D), and review the literature on the clinical characteristics and gene mutations of FBP1D in the Chinese population. A FBP1D proband due to variant of FBP1 gene who was admitted to Women and Children's Hospital of Ningbo University on August 10, 2021 due to "vomiting for 1 day" was selected as the study subject. Clinical data of the child were retrospectively collected. Whole exome sequencing (WES) was performed on the child, and candidate variants identified in the child were validated by Sanger sequencing in both the child and his parents. The difference between wild type and variant FBP1 protein were compared using AlphaFold v3.0.1 and PyMOL v2.5.6. The pathogenicity of candidate variant was rated according to the Standards and Guidelines for the Interpretation of Sequence Variants released by American College of Medical Genetics and Genomics (ACMG) (hereinafter referred to as ACMG guidelines). Using keywords such as "FBP1 gene" and "fructose-1,6-bisphosphatase deficiency" both in Chinese and English, relevant literature on FBP1D patients caused by FBP1 gene variants in the Chinese population were retrieved from the PubMed database, CNKI, and Wanfang Data Knowledge Service Platform, and the genetic variant and clinical phenotypes of FBP1D patients reported in the literature were analyzed. The literature retrieval time was set from the establishment of each database to October 31st, 2024. This study was approved by the Women and Children's Hospital of Ningbo University (Ethics No.: 2020-048). The proband was presented with repeated infections, nausea, vomiting, and mental illness. The auxiliary examination revealed hypoglycemia, acidosis, liver and kidney dysfunction, hyperlipidemia and hepatomegaly. WES and Sanger sequencing revealed that the child has harbored compound heterozygous variants of the FBP1 gene, including a de novo nonsense variant c.778G>T (p.G260*) in exon 6 and a maternally derived missense variant c.923C>G (p.P308R) in exon 7. The c.923C>G was known as a likely pathogenic variant, while c.778G>T has not been included in the databases such as HGMD, ClinVar, 1000 Genomes, ExAC, dbSNP, and gnomAD. Protein structure prediction shows that the c.778G>T (p.G260*) variant may result in a premature termination codon, resulting in loss of a β-fold in a core region, which may significantly reduce the stability of its protein product and affect its function. Based on the ACMG guidelines, the c.778G>T (p.G260*) variant was rated as likely pathogenic (PVS1_Strong+PM2_Supporting+PP4+PM6). Literature review has identified 32 patients from 23 Chinese families with FBP1D due to FBP1 gene variants. Together with the case reported in this study, in total 33 patients were analyzed. Among them, 22 cases were males (66.7%) with hypoglycemia, metabolic acidosis, vomiting, seizures, hyperlactatemia, and ketosis as the primary clinical phenotypes. After treatment, only 1 case (3.0%) died due to cerebral hernia, while the remaining 32 (97.0%) had favorable outcomes. Four cases (12.1%) exhibited developmental delay. A total of 66 FBP1 gene variant sites were identified, which involved 22 variant types, predominantly missense mutations (31 gene variant sites). These variants were mainly located in exon 7 of the gene (25 variant sites), with c.490G>A (16.7%, 11/66), c.960_961insG (19.7%, 13/66), c.355G>A (12.1%, 8/66), and c.704delC (9.1%, 6/66) being the most common variants. The heterozygous variant of the FBP1 gene probably underlay the FBP1D in this child. Above finding has enriched the phenotypic and mutational spectrum of the FBP1 gene and provided a basis for genetic counseling and clinical decision-making.

To explore the genotype-phenotype correlation in a Charcot-Marie-Tooth type 2A2A (CMT2A2A) pedigree and to provide genetic counseling for its subsequent pregnancies. A Chinese pedigree presenting with "lower limb muscle atrophy and movement disorders" at the Prenatal Diagnosis Center of Xuzhou Central Hospital between January and August 2024 was selected as the study subject. Relevant clinical data were collected from the pedigree members. Peripheral blood samples from affected individuals, and amniotic fluid and/or chorionic villus samples were obtained for DNA extraction. Whole exome sequencing (WES) was carried out. Candidate variants were verified by Sanger sequencing. Pathogenicity assessment and bioinformatic analysis were conducted. This study was approved by the Medical Ethics Committee of Xuzhou Central Hospital (Ethics No. XZXY-LK-20240111-0019). All affected individuals in this pedigree were females, whom included the proband, her mother, and her first daughter. Earlier age of onset was associated with more severe lower limb atrophy. A heterozygous missense variant of the MFN2 gene, namely c.314C>T (p.Thr105Met), was identified in the proband, her mother, daughter, and the third fetus from a re-marriage. The same variant was absent in her elder brother, current husband, and her fourth fetus. Based on the guidelines from American College of Medical Genetics and Genomics (ACMG) and recommendations from Clinical Genome Resources (ClinGen), the variant was classified as pathogenic (PP1_Strong+PM1+PS3+PS4_Moderate+PP3_Moderate+PM2_Supporting). Analyses with PROVEAN and Mutation Taster had categorized the variant as "deleterious" and "disease-causing", respectively. Analysis with Uniprot and Jalview showed that the affected amino acid residue is conserved across multiple species. ChEBI software predicted that the variant may alter the polarity of the 105th amino acid residue. The c.314C>T (p.Thr105Met) missense variant of the MFN2 gene probably underlie the CMT2A2A in this pedigree. Above finding has enabled prenatal diagnosis and genetic counseling for its subsequent pregnancies.

One is the loneliest number: genotypic matchmaking using the electronic health record

To explore the clinical phenotype and genetic characteristics of a pediatric child with RELA-associated autoinflammatory disease (RAID) caused by a RELA gene variant, and to review the reported cases in the literature. A pediatric child with RAID who presented with recurrent fever, vomiting, and oral ulcers for over 5 years was selected as the study subject. The child visited the Women and Children's Hospital of Ningbo University in August 2023. Clinical data were collected, and peripheral blood samples were obtained from the child and his family members for whole-exome sequencing (WES) and Sanger sequencing to identify and validate candidate variants. The pathogenicity of the variants was analyzed accordingly. Using the keywords "RELA" "NF-κB" "autoinflammatory disease" "tofacitinib" "sulfasalazine" a literature search was conducted in the China National Knowledge Infrastructure, Wanfang Data Knowledge Service Platform, and PubMed from January 1, 2000 to December 13, 2023. This study was approved by the Medical Ethics Committee of the Women and Children's Hospital of Ningbo University (Ethics No. EC2020-048). The child primarily manifested with recurrent fever, vomiting, and oral ulcers. WES identified a heterozygous nonsense variant c.985C>T (p.Arg329Ter) in the RELA gene, which was inherited from the mother. According to the American College of Medical Genetics and Genomics (ACMG) Standards and Guidelines for the Interpretation of Sequence Variants and the Clinical Genome Resource (ClinGen) recommendations for PVS1, this variant was classified as pathogenic (PVS1+PM2_Supporting+PP4). Despite treatment with adalimumab and tocilizumab, the child's symptoms persisted. Switching to tofacitinib improved oral ulcers, but fever and vomiting continued. The addition of thalidomide significantly alleviated fever and vomiting, and the patient's growth and development remained normal. A literature review identified 14 unrelated RAID families, including a total of 35 cases (including the present child). The main clinical features were recurrent oral ulcers, genital ulcers, skin problems, fever, diarrhea, abdominal pain, and vomiting. The nonsense variant c.985C>T (p.Arg329Ter) in the RELA gene is likely the genetic cause of the child's recurrent fever, vomiting, and oral ulcers. WES is valuable for timely diagnosis of RAID and provides a basis for clinical treatment strategies.

To explore the clinical features of a child with Lamb-Shaffer syndrome (LAMSHF) due to a variant of SOX5 gene. A child who was admitted to Children's Hospital Affiliated to Zhengzhou University in July 2022 was selected as the study subject. Clinical data of the child was collected. Whole exome sequencing (WES) was carried out on peripheral blood samples from the child and his parents, and candidate variant was verified by Sanger sequencing and bioinformatic analysis. The study has been approved by the Medical Ethics Committee of the Children's Hospital Affiliated to Zhengzhou University (Ethics No. 2024-K-100). The child, an one-year-and-seven-month-old male, has manifested delayed development in speech and language, intelligence and movement, in addition with mild facial deformities and eye signs. Whole exome sequencing revealed that he has harbored a heterozygous c.1828_1829insGACT (p.Y610fs*1) frameshifting variant of the SOX5 gene. Sanger sequencing confirmed the variant to be de novo in origin. The variant was also unreported previously. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), the variant was rated as pathogenic (PVS1+PS2+PM2_supporting). The c.1828_1829insGACT (p.Y610fs*1) variant of the SOX5 gene probably underlay the pathogenesis of LAMSHF in this child. For children with delayed mental, language, intellectual, and motor development, genetic testing should be conducted to facilitate early diagnosis. Above finding has enriched the mutational spectrum of the SOX5 gene.

Does the law require reinterpretation and return of revised genomic results?

DNA-based screening and personal health: a points to consider statement for individuals and health-care providers from the American College of Medical Genetics and Genomics (ACMG)