Correction: Suppression of Mitochondrial Complex I Influences Cell Metastatic Properties.

[This corrects the article DOI: 10.1371/journal.pone.0061677.].

Activated phosphoinositide 3-kinase δ syndrome caused by PIK3CD mutations: expanding the phenotype.

BACKGROUND: Germline heterozygous gain-of-function (GOF) mutations in the PIK3CD gene lead to a rare primary immunodeficiency disease known as activated phosphoinositide 3-kinase (PI3K) δ syndrome type 1(APDS1). Affected patients present a spectrum of clinical manifestations, particularly recurrent respiratory infections and lymphoproliferation, increased levels of serum immunoglobulin (Ig) M, Epstein-Barr virus (EBV) and cytomegalovirus (CMV) viremia. Due to highly heterogeneous phenotypes of APDS1, it is very likely that suspected cases may be misdiagnosed. METHODS: Herein we reported three patients with different clinical presentations but harboring pathogenic variants in PIK3CD gene detected by trio whole-exome sequencing (trio-WES) and confirmed by subsequent Sanger sequencing. RESULTS: Two heterozygous mutations (c.3061G > A, p.E1021K and c.1574 A > G, p.E525G) in PIK3CD (NM_005026.3) were identified by whole exome sequencing (WES) in the three patients. One of two patients with the mutation (c.3061G > A) presented with abdominal pain and diarrhea as the first symptoms, which was due to intussusception caused by multiple polyps of colon. The patient with mutation (c.1574 A > G) had an anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV)-like clinical manifestations, including multisystemic inflammation, acute nephritic syndrome, and positive perinuclear ANCA (p-ANCA), thus the diagnosis of ANCA-AAV was considered. CONCLUSIONS: Our study expands the spectrums of clinical phenotype and genotype of APDS, and demonstrates that WES has a high molecular diagnostic yield for patients with immunodeficiency related symptoms, such as respiratory infections, multiple ecchymosis, ANCA-associated vasculitis, multiple ileocecal polyps, hepatosplenomegaly, and lymphoid hyperplasia. TRIAL REGISTRATION: Retrospectively registered.

Identification and characterization of a new variation in DPM2 gene in two Chinese siblings with mild intellectual impairment.

Introduction: Congenital disorders of glycosylation (CDGs) are a genetically heterogeneous group of metabolic disorders caused by abnormal protein or lpid glycosylation. DPM2 is one subunit of a heterotrimeric complex for dolichol-phosphatemannose synthase (DPMS), a key enzyme in glycosylation, and only four patients with DPM2-CDG have been reported. Methods: Whole-exome sequencing (WES) was performed in a Chinese family having two siblings with a mild form of DPM2-CDG with developmental delay, mild intellectual disability, hypotonia, and increased serum creatine kinase. Sanger sequencing was used to validate the variants identified in the siblings and their parents. In vitro functional study was performed. Results: A homozygous mutation, c.197G>A (p.Gly66Glu) in exon 4 of DPM2 (NM_003863) was identified by whole exome sequencing (WES). In vitro functional analysis demonstrated that this variant increased the expression level of DPM2 protein and western blot revealed a significant decrease in ICAM1, a universal biomarker for hypoglycosylation in patients with CDG, suggesting abnormal N-linked glycosylation. We also reviewed the 4 previously reported patients carrying homozygous or compound heterozygous variants of DMP2 gene, and found that patients with variants within the region encoding the first domain had more severe clinical symptoms than those with variants within the second domain. However, the actual genotype-phenotype relationship needs more study. Discussion: Overall, our study broadens the variant spectrum of DPM2 gene, attempts to explain the different phenotypes in patients with different DPM2 variants, and emphasizes the need of further functional studies to understand the underlying pathophysiology of the phenotypic heterogeneity.

Clinical features of CNOT3-associated neurodevelopmental disorder in three Chinese patients.

CNOT3 is the central component of the CCR4-NOT protein complex, which is a global regulator of RNA polymerase II transcription. Loss of function mutations in CNOT3 lead to intellectual developmental disorder with speech delay, autism, and dysmorphic facies (IDDSADF), which is very rare. Herein, we reported two novel heterozygous frameshift mutations (c.1058_1059insT and c.724delT) and one novel splice site variant (c.387 + 2 T > C) in CNOT3 (NM_014516.3) gene in three Chinese patients with dysmorphic features, developmental delay, and behavior anomalies. The functional study showed that the CNOT3 mRNA levels were significantly decreased in the peripheral blood of two patients with c.1058_1059insT and c.387 + 2 T > C variants, respectively, and minigene assay demonstrated that the splice variant (c.387 + 2 T > C) resulted in exon skipping. We also found that CNOT3 deficiency was linked to alterations of expression levels of other CCR4-NOT complex subunits in mRNA level in the peripheral blood. By analyzing the clinical manifestations of all these patients with CNOT3 variants, including our three cases and 22 patients previously reported, we did not observe a correlation between genotypes and phenotypes. In summary, this is the first time to report cases with IDDSADF in the Chinese population, and three novel CNOT3 variants in these patients expand its mutational spectrum.

Identification of a novel TNNI3 synonymous variant causing intron retention in autosomal recessive dilated cardiomyopathy.

BACKGROUND: Dilated cardiomyopathy type 2A (DCM2A, MIM: #611880) is a rare autosomal recessive heart disease leading to heart failure and sudden cardiac death. However, the causative role of TNNI3 in DCM2A is still questioned due to few cases reported and the conflicting molecular biological evidence. METHODS: Trio whole-exome sequencing (trio-WES) was performed in a Chinese family with dilated cardiomyopathy. Sanger sequencing and real-time quantitative PCR were used to confirm the variants identified. Expression outcome caused by the synonymous mutation was validated by minigene splicing analyses. RESULTS: The one-year-old girl presented severe left ventricular enlargement and significantly reduced left ventricular systolic function and she died of respiratory and heart failure soon after her diagnosis. Trio-WES revealed a compound heterozygous variants of TNNI3, a novel c.24G＞A (p.Ala8Ala) (NM_000363.4) in exon 2 and a deletion of entire gene. Minigene splicing analyses showed it led to an intron retention (c.24 + 1_24 + 45ins) by intron 2 cryptic splicing. CONCLUSIONS: Our study describes and characterizes a synonymous mutation in TNNI3 gene, supporting the clinical diagnosis of an autosomal recessive DCM. Our study emphasizes the importance of functional analysis to assess the potential pathogenicity of synonymous mutations, especially when the synonymous variants are not annotated as benign.

Corrigendum: Identification of the first congenital ichthyosis case caused by a homozygous deletion in the ALOX12B gene due to chromosome 17 mixed uniparental disomy.

[This corrects the article DOI: 10.3389/fgene.2022.931833.].

A novel variant in the HX repeat motif of ATN1 in a Chinese patient with CHEDDA syndrome and literature review.

BACKGROUND: CHEDDA syndrome is a rare neurodevelopmental syndrome caused by heterozygous missense or indel variants in the HX repeat motif of ATN1 gene. To date, CHEDDA has been identified in a few ethnic groups, and only 17 patients have been reported in literature, and no case has been reported in any country or region in Asia. METHODS: Trio-exome sequencing (Trio-ES) examination was conducted in a Chinese girl with global developmental delay and in her parents. Sanger sequencing was performed to confirm the candidate variant. RESULTS: This patient presented with mental and motor developmental delay, speech delay, and mild dysmorphic facial features, and had no epilepsy and visual impairment. Brain MRI did not show obvious structural abnormality. Through ES we identified a novel and de novo variant, c.3176_c.3177insGCACCT (p.Ser1059_His1060insHisLeu), within the HX motif of ATN1. No other pathogenic variant in another gene was found to support an alternative clinical and molecular diagnosis. CONCLUSIONS: This is the first described case of CHEDDA from China. Together with the available literature data, we found that either disruption of HX motif or alteration of the HX repeat number would lead to ATN1-associated CHEDDA. We also noted that CHEDDA is a clinical heterogenous syndrome, and patients carrying the same or similar variant might have different clinical manifestations and prognosis.

A novel CARD11 germline mutation in a Chinese patient of B cell expansion with NF-κB and T cell anergy (BENTA) and literature review.

Germline gain-of-function (GOF) mutations in the CARD11 gene lead to a rare primary immunodeficiency disease known as B cell expansion with NF-κB and T cell anergy (BENTA). Affected patients present with a polyclonal expansion of B cells, lymphadenopathy, and splenomegaly. Herein, we report a novel germline in-frame three base-pair deletion (c.1030_1032del, p.K344del) in the CARD11 gene in a patient with atypical BENTA, presenting with a recurrent fever and B cell lymphocytosis. This mutation was inherited from his mother, who is clinically asymptomatic and had a recurrent respiratory tract infection in her childhood. In vitro functional analysis demonstrated that this variant decreased the expression level of the CARD11 protein and activated the NF-κB signal pathway, leading to a higher expression of several NF-κB target gene transcripts in HCT116 cells transfected with mutant CARD11 (K344del-CARD11) as revealed by RNA sequencing analysis. To our knowledge, only 23 BENTA patients have been identified and carried seven distinct GOF mutations in CARD11. The clinical manifestations of patients are highly heterogeneous and there was no significant correlation between genotype and phenotype. In summary, we identified a novel in-frame three base-pair deletion that may be responsible for the pathogenesis of atypical BENTA in a Chinese family. Our study expands the mutational spectrum of the CARD11 gene and may be helpful in the understanding of diseases caused by CARD11 mutations and the clinical management of BENTA.

Identification of the first congenital ichthyosis case caused by a homozygous deletion in the ALOX12B gene due to chromosome 17 mixed uniparental disomy.

Uniparental disomy (UPD) is a rare genetic event caused by errors during gametogenesis and fertilization leading to two copies of a chromosome or chromosomal region inherited from one parent. MixUPD is one type of UPD that contains isodisomic and heterodisomic parts because of meiotic recombination. Using whole-exome sequencing (WES), we identified the first case of ichthyosis due to a maternal mixUPD on chromosome 17, which results in a homozygous deletion of partial intron 8 to exon 10 in ALOX12B, being predicted to lead to an internal protein deletion of 97 amino acids. We also performed a retrospective analysis of 198 patients with ALOX12B mutations. The results suggested that the exon 9 and 10 are located in the mutational hotspots of ALOX12B. In addition, our patient has microtia and congenital stenosis of the external auditory canals, which is very rare in patients with ALOX12B mutations. Our study reports the first case of autosomal recessive congenital ichthyosis (ARCI) due to a mixUPD of chromosome 17 and expands the spectrum of clinical manifestations of ARCI caused by mutations in the ALOX12B gene.

Infantile-onset CMT2D/dSMA-V in a Chinese family with parental germline mosaicism for a novel mutation in the GARS1 gene.

BACKGROUND AND AIMS: Both Charcot-Marie-Tooth disease type 2D (CMT2D) and distal spinal muscular atrophy type V (dSMA-V) are GARS1 disease phenotypes involving axonal peripheral neuropathy. Patients often develop clinical symptoms in their teens. Herein, we reported a Chinese family with infantile-onset CMT2D/dSMA-V. METHODS: Clinical evaluation and laboratory examination were performed in our proband, the older sister from this family, and trio exome sequencing (ES) was conducted on the proband and her parents, followed by Sanger sequencing. RESULTS: A novel GARS1 mutation (c.997G>C, p.E333Q; NM_002047) was identified in this patient and her younger sister but not in her parents; thus, it is presumed that this mutation is inherited from a germline mosaic parent. The younger sister began to exhibit weakness of her hands and feet at the age of 1 year old. CONCLUSION: This is the first report of infantile CMT2D/dSMA-V in China. Our study increases the number of infantile-onset cases, as well as reported pathogenic variants in the GARS1 gene, and highlights the important role of exome sequencing in the clinical diagnosis of disease and enabling subsequent prenatal diagnosis. Our study reminds us to consider the possibility of parent germline mosaicism in the subsequent prenatal genetic diagnosis when identifying a de novo variant.

[Clinical features and genetic analysis of a case with Perlman syndrome due to variant of DIS3L2 gene].

OBJECTIVE: To analyze the clinical phenotype and genetic characteristics of a child with Perlman syndrome. METHODS: Genomic DNA was extracted from peripheral blood samples from the patient and her parents. Whole exome sequencing (WES) was carried out to detect potential variant in the proband. Candidate variant was verified by Sanger sequencing. The pathogenicity of candidate variants was evaluated according to the guidelines of the American College of Medical Genetics and Genomics (ACMG). RESULTS: The results of WES showed that the proband has harbored compound heterozygous variants of the DIS3L2 gene, namely c.2109delC and c.1829.c.1830insC, which were respectively inherited from her mother and father. The results were confirmed by Sanger sequencing. Based on the ACMG guidelines, the two novel variants were both predicted to be pathogenic (PVS1+PS2+PM2). CONCLUSION: The compound heterozygous variants of the DIS3L2 gene probably underlay the Perlman syndrome in this patient. Above finding has enriched the spectrum of DIS3L2 gene mutations.

Identification and Characterization of a Germline Mutation in CARD11 From a Chinese Case of B Cell Expansion With NF-κB and T Cell Anergy.

B cell expansion with NF-κB and T cell anergy (BENTA) is a rare primary immunodeficiency disorder caused by gain-of-function (GOF) mutations in the CARD11 gene. Affected patients present with persistent B cell lymphocytosis in early childhood paired with lymphadenopathy and splenomegaly. Until now only six activating mutations from 14 patients have been reported in CARD11. Here we report a patient from China with polyclonal B cell lymphocytosis and frequent infections in early life. A heterozygous mutation (c.377G>A, G126D) in exon 5 of CARD11 gene (NM_032415) was identified by whole exome sequencing. In vitro functional studies showed that the G126D mutation is associated with increased expression of CARD11 and NF-κB activation in Hela cells. Flow cytometry analysis indicated NK cell activity and CD107a degranulation of the patient were decreased. RNA sequencing analysis showed that a number of genes in NF-κB pathway increased while those involved in NK cell activity and degranulation were down-regulated. In summary, our work identified a de novo germline GOF mutation in CARD11 with functional evidence of BENTA.

Three de novo variants in KMT2A (MLL) identified by whole exome sequencing in patients with Wiedemann-Steiner syndrome.

BACKGROUND: Wiedemann-Steiner syndrome (WSS) is an autosomal dominant disorder characterized by short stature, hypertrichosis, intellectual disability, developmental delay, along with facial dysmorphism. WSS patients exhibit great phenotypic heterogeneities. Some variants in KMT2A (MLL) gene have been identified as the cause of WSS. METHODS: Whole exome sequencing on the probands followed by Sanger sequencing validations in the family were applied to determine genetic variants. In silico analyses were used for predicting potential effects of the variants. RESULTS: We identified three novel de novo heterozygous variants: c.883A>T (p.Lys295*), c.4171C>T (p.Gln1391*), and c.3499T>C (p.Cys1167Arg), in KMT2A gene from three unrelated Chinese WSS patients. According to the American College of Medical Genetics and Genomics (ACMG) guidelines, these three variants were classified as pathogenic, pathogenic and likely pathogenic variant, respectively. By reviewing all the available cases with same mutated KMT2A regions as the three patients had, we found that in addition to the representative symptoms, our patients exhibited some sporadically observed symptoms, such as severe ophthalmological symptoms, endocardial fibroelastosis, cytomegalovirus infection, and feet eversion. We also revealed that variants in different KMT2A regions contribute to the phenotypic heterogeneity of WSS, highlighting challenges in the diagnosis of syndromic disorders spanning a broad phenotypic spectrum. CONCLUSION: Our study would aid in further broadening our knowledge about the genotype-phenotype correlation of WSS.

[Novel duplication mutation of EYA1 causes branchio-oto-renal syndrome in a Chinese family].

Objective:To identify novel genetic causes of branchio-oto-renal （BOR） syndrome in a Chinese family. Methods:Clinical characteristics and treatment of a family with a BOR syndrome were retrospectively analyzed. Genetic analysis was conducted by trio whole exome sequencing （WES） and the duplicated exons were verified by fluorescence quantitative PCR （real-time PCR）. Results: In this family, the affected individual had deafness, structural malformation of inner ear and middle ear, pre-auricular fistula, cervical fistula and renal atrophy consistent with the clinical diagnosis of BOR syndrome. Neither the father nor the mother had similar phenotype. WES and quantitative fluorescent PCR revealed that the patient had a de novo partial duplication involving exons 13 to 18 of EYA1 gene. This mutation has not been reported in literature or any database. Bilateral pre-auricular fistulas and cervical fistulas were surgically removed and the surgery wound healed well, while hearing AIDS had been worn to assist hearing. Conclusion:This study is the first to detect a novel de novo partial duplication （exons13-18） of EYA1 gene leading to BOR syndrome, and expands the mutant spectrum of EYA1 gene in Chinese population.

Genetic analysis and prenatal diagnosis in a Chinese with growth retardation, abnormal liver function, and microcephaly.

BACKGROUND: Congenital disorders of glycosylation (CDG) are a genetically heterogeneous group of disorders caused by defects in the synthesis and processing of glycoproteins. COG6-CDG is a kind of disorder caused by conserved oligomeric golgi complex 6 (COG6) deficiency. To date, only 19 patients with COG6-CDG have been reported. METHODS: We report a girl in a Chinese family with developmental delay, growth retardation, microcephaly, abnormal liver function, and hypohidrosis. Trio whole-exome sequencing was performed for this patient and her parents, and the variants identified were validated by Sanger sequencing. Prenatal diagnosis was done for this family during a subsequent pregnancy. The literature review on these patients was performed by reviewing articles published in English and Chinese. RESULTS: Genetic sequencing identified two novel heterozygous mutations: c.428G>T (p.S143I) and c.1843C>T (p.Q615X) in the COG6 gene, inherited from her healthy parents, respectively. A total of 11 different mutations in COG6 have been reported previously, and mutations potentially affecting splicing are the most common. The main clinical features included development delay, facial dysmorphism, growth retardation, skin abnormalities (hypohidrosis), microcephaly, abnormal brain structure, liver involvement, and recurrent infections. CONCLUSION: Our work broadens the mutation spectrum of COG6 gene and states the importance of whole-exome sequencing in facilitating the definitive diagnosis of this disorder and prenatal diagnosis in a subsequent pregnancy.

Influence of UGT2B7 and UGT1A6 polymorphisms on plasma concentration to dose ratio of valproic acid in Chinese epileptic children.

We explored the potential effects of genetic variations on the concentration to dose ratio (CDR) of valproic acid (VPA) in paediatric epilepsy patients.Two hundred and twenty-nine epileptic children on VPA monotherapy were included, and the VPA trough concentrations at steady-state of all subjects were determined.Nineteen single nucleotide polymorphisms (SNPs) of seven selected genes related to the metabolising enzymes and transporters of VPA were identified, and their influences on CDRVPA (a logarithmic transformation was performed if abnormally distributed) were evaluated.UGT2B7 rs7668258 (C>T) TT genotype was associated with a decrease in lnCDRVPA among epileptic children receiving VPA monotherapy (ß=-0.191, p = 0.036). Significantly lower lnCDRVPA was also observed in paediatric patients with UGT1A6 rs2070959 (A>G) GG genotype compared to those AA genotype (ß=-0.270, p = 0.021).This research indicated that UGT2B7 rs7668258 (C>T) and UGT1A6 rs2070959 (A>G) polymorphisms may be correlated to the normalised plasma concentrations of VPA in Chinese epileptic children. The associations could be abolished after Bonferroni's correction and our findings need to be validated in further and larger investigations.

A 9-month-old Chinese patient with Gabriele-de Vries syndrome due to novel germline mutation in the YY1 gene.

BACKGROUND: Gabriele-de Vries syndrome (GADEVS), also known as YY1 haploinsufficiency syndrome, is a very rare autosomal dominant neurodevelopmental disorder (NDD) due to YY1 mutation characterized by mild-to-profound developmental delay (DD)/intellectual disability (ID), a wide spectrum of functional and morphologic abnormalities, and intrauterine growth restriction or low birth weight and feeding difficulties are common in the patients. However, NDDs, such as language development disorder and ID, could hardly be assessed in patients younger than 2 years old. METHODS: We describe a 9-month-old female with DD, failure to thrive, and facial dysmorphism. Genetic analysis was conducted by whole exome sequencing (WES) and confirmed by Sanger sequencing. RESULTS: In addition to DD and dysmorphic facial features, this patient had urinary tract infection, acute pyelonephritis, bilateral vesicoureteral reflux (grade III), gastroesophageal reflux, and malnutrition. She was found to have foramen ovale or atrial septal defect, and enlarged left lateral ventricle in the brain. After performing WES, a novel heterozygous mutation NM_003403.5:c.1124G>A, p.Arg375Gln in the YY1 gene was identified. CONCLUSION: Our findings suggest that genetic tests are critical technique for diagnosis of GADEVS, especially in patients with early-childhood, unexplained developmental or growth disorders, thus, the prevalence of GADEVS may be underestimated. The clinical features and identified YY1 mutation in our patient expand the spectra of phenotypes and genotypes of GADEVS, respectively.

Effects of SCN1A and SCN2A polymorphisms on responsiveness to valproic acid monotherapy in epileptic children.

PURPOSE: This study was conducted to explore the influence of genetic variations on responsiveness to valproic acid (VPA) monotherapy among Chinese children with epilepsy. METHODS: One hundred and forty epileptic children taking VPA as monotherapy were enrolled, and at least one-year follow-up was obtained to assess the therapeutic outcome. Twenty-seven single nucleotide polymorphisms (SNPs) within twelve candidate genes correlated with the metabolic enzymes, transporters and targets of VPA were genotyped. The effects of selected polymorphisms on VPA efficacy were identified by binary logistic regression analysis adjusting for potential confounders. RESULTS: SCN2A rs2304016 (A > G) AG genotype was more common among the VPA-resistant patients in comparison with the VPA-responsive patients (OR = 3.18, 95 % CI = 1.10-9.14, P = 0.032), and in subgroup of focal seizure, lower frequency of VPA resistance was found in epileptic children with SCN1A rs2298771 AG genotype than those with AA genotype (OR = 0.11, 95 % CI = 0.01-0.91, P = 0.040). CONCLUSIONS: Our study indicated that SCN2A rs2304016 and SCN1A rs2298771 polymorphisms might be associated with the response to VPA monotherapy in Chinese epileptic children. Further and larger researches are required to validate these results.