Compound heterozygous variants in POR gene identified by whole-exome sequencing in a Chinese pedigree with cytochrome P450 oxidoreductase deficiency

In Silico Analysis of PORD Mutations on the 3D Structure of P450 Oxidoreductase

Cytochrome P450 oxidoreductase (POR) is a membrane-bound flavoprotein that helps in transferring electrons from its NADPH domain to all cytochrome P450 (CYP450) enzymes. Mutations in the POR gene could severely affect the metabolism of steroid hormones and the development of skeletal muscles, a condition known as Cytochrome P450 oxidoreductase deficiency (PORD). PORD is associated with clinical presentations of disorders of sex development, Antley and Bixler’s syndrome (ABS), as well as an abnormal steroid hormone profile. We have performed an in silico analysis of POR 3D X-ray protein crystal structure to study the effects of reported mutations on the POR enzyme structure. A total of 32 missense mutations were identified, from 170 PORD patients, and mapped on the 3D crystal structure of the POR enzyme. In addition, five of the missense mutations (R457H, A287P, D210G, Y181D and Y607C) were further selected for an in-depth in silico analysis to correlate the observed changes in POR protein structure with the clinical phenotypes observed in PORD patients. Overall, missense mutations found in the binding sites of POR cofactors could lead to a severe form of PORD, emphasizing the importance of POR cofactor binding domains in transferring electrons to the CYP450 enzyme family.

Antley-Bixler syndrome arising from compound heterozygotes in the P450 oxidoreductase gene: a case report

Antley-Bixler syndrome (ABS) arising from P450 oxidoreductase deficiency (PORD) is a rare, distinct craniosynostosis syndrome, accompanied by ambiguous genitalia and impaired steroidogenesis. It is reported that this disorder is caused by mutations in the P450 oxidoreductase (POR; OMIM #124015) gene via autosomal recessive inheritance. In this study, we performed a molecular analysis to verify the genetic etiology of ABS in an infant. Initially, medical exome sequencing was applied using the parents' peripheral blood genome DNA. Next, bidirectional Sanger sequencing and quantitative real-time PCR (qRT-PCR) were conducted to confirm the sequencing results. The infant was diagnosed as ABS at birth, with typical midface hypoplasia, craniosynostosis, femoral bowing, radio-ulnar synostosis, and genital anomalies. She died two months later due to severe pneumonia and congenital heart disease. The medical exome sequencing and Sanger sequencing revealed the missense mutation c.1370G>A (p.R457H) in exon 12 of POR was inherited from the father. In addition, the qRT-PCR analysis verified an exon 5 microdeletion in the POR gene of the infant and her mother. While p.R457H is a well-known pathogenic mutation, the POR exon 5 deletion is absent from the public databases. However, it is classified as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines based on the evidence of PVS1, PM2, and PM3. In conclusion, this infant with ABS carried compound heterozygotic mutations in the POR gene; one was a paternal missense mutation, and the other was a maternal novel microdeletion. The mutations were inherited from the paternal grandfather and maternal grandfather, respectively. This detailed case report enriches our knowledge of the POR mutation spectrum and ABS pathogenesis.

Novel Neonatal Variants of the Carbamoyl Phosphate Synthetase 1 Deficiency: Two Case Reports and Review of Literature

Carbamoyl phosphate synthetase I (CPS1) deficiency (CPS1D), is a rare autosomal recessive disorder, characterized by life-threatening hyperammonemia. In this study, we presented the detailed clinical features and genetic analysis of two patients with neonatal-onset CPS1D carrying two compound heterozygous variants of c.1631C > T (p.T544M)/c.1981G > T (p.G661C), and c.2896G > T (p.E966X)/c622-3C > G in CPS1 gene, individually. Out of them, three variants are novel, unreported including a missense (c.1981G > T, p.G661C), a nonsense (c.2896G > T, p.E966X), and a splicing change of c.622-3C > G. We reviewed all available publications regarding CPS1 mutations, and in total 264 different variants have been reported, with majority of 157 (59.5%) missense, followed by 35 (13.2%) small deletions. This study expanded the mutational spectrum of CPS1. Moreover, our cases and review further support the idea that most (≥90%) of the mutations were "private" and only ∼10% recurred in unrelated families.

Correlation between TERT C228T and clinic-pathological features in pediatric papillary thyroid carcinoma

The aims of the present study were to reveal the prevalence of the TERT C228T mutation in pediatric papillary thyroid carcinoma (PPTC) and to further investigate the role of the TERT C228T mutation in PPTC. We also tested another TERT mutation, TERT C250T, although this was not detected in PPTC patients. In this study, 48 patients with PPTC (41 with classic PPTC) were enrolled. DNA was extracted from PPTC tissues and TERT C228T mutation analysis was performed. Chi-squared analysis, Fisher's exact test, and a t-test were applied to test the significance of differences. The TERT C228T mutation presented in 13 (27.1%) of the 48 PPTC patients and 10 (24.4%) of the 41 classical PPTC patients. There were significant differences between PPTC patients with the TERT C228T mutation and those without in terms of modified radical neck dissection, multifocality, capsular invasion, extrathyroidal invasion, and American Joint Committee on Cancer (AJCC) tumor stage (P<0.05). In classical PPTC, there were additional significant differences in other clinic-pathological features, such as AJCC nodal stage (P=0.009) and American Thyroid Association (ATA) PPTC stage (P=0.021) between patients with and without the TERT C228T mutation. These findings indicate that the TERT C228T mutation is significantly correlated with certain aggressive clinic-pathological features of PPTC.

Phenotype-Driven Virtual Panel Is an Effective Method to Analyze WES Data of Neurological Disease

Objective: Whole Exome Sequencing (WES) is an effective diagnostic method for complicated and multi-system involved rare diseases. However, annotation and analysis of the WES result, especially for single case analysis still remain a challenge. Here, we introduce a method called phenotype-driven designing "virtual panel" to simplify the procedure and assess the diagnostic rate of this method. Methods: WES was performed in samples of 30 patients, core phenotypes of probands were then extracted and inputted into an in-house software, "Mingjian" to calculate and generate associated gene list of a virtual panel. Mingjian is a self-updating genetic disease computer supportive diagnostic system that based on the databases of HPO, OMIM, HGMD. The virtual panel that generated by Mingjian system was then used to filter and annotate candidate mutations. Sanger sequencing and co-segregation analysis among the family were then used to confirm the filtered mutants. Result: We first used phenotype-driven designing "virtual panel" to analyze the WES data of a patient whose core phenotypes are ataxia, seizures, esotropia, puberty and gonadal disorders, and global developmental delay. Two mutations, c.430T > C and c.640G > C in PMM2 were identified by this method. This result was also confirmed by Sanger sequencing among the family. The same analysing method was then used in the annotation of WES data of other 29 neurological rare disease patients. The diagnostic rate was 65.52%, which is significantly higher than the diagnostic rate before. Conclusion: Phenotype-driven designing virtual panel could achieve low-cost individualized analysis. This method may decrease the time-cost of annotation, increase the diagnostic efficiency and the diagnostic rate.