Human Mutation最新文献

Affecting fewer than 20,000 people as defined in South Korea, rare diseases pose significant diagnostic challenges due to their diverse manifestations and genetic heterogeneity. Genome sequencing (GS) offers a promising solution by enabling simultaneous screening for thousands of rare genetic disorders. This study explores the diagnostic utility and necessity of GS within the government-funded Korean Regional Rare Disease Diagnostic Support Program (KR-RDSP), a collaborative initiative involving 11 regional rare disease centers across Korea. The program was launched as a proof-of-concept study in 2023 to equip the genetic clinics with a diagnostic tool to expedite the diagnoses for rare disease patients who reside outside the urban Seoul region where diagnostic resources are limited. The study leveraged GS to diagnose a cohort of 400 patients exhibiting a wide spectrum of symptoms. The overall diagnostic yield was 36.3% (145/400), with 4.8% (7/145) of the diagnosed patients being reported with variants that could not have been identified by chromosomal microarray or exome sequencing (ES), highlighting the added value of comprehensive genomic analysis. The implementation of a centralized GS analysis system streamlined the diagnostic process, enabling timely reporting within a reasonable turnaround time of ≤ 35 days. Segregation analysis by Sanger sequencing played a crucial role in confirming or reclassifying variant pathogenicity by elucidating inheritance patterns. Here, we summarize diagnostic statistics from the 400 GS dataset gathered from June 2023 to December 2023 and show interesting and informative case examples that illustrate the diagnostic efficacy of GS, highlighting its ability to uncover elusive genetic etiologies and provide personalized treatment insights. The study also highlights the successful implementation of the program for the 11 regional rare disease centers across Korea with a practical workflow, comprehensive testing, comparable diagnostic yield to previous reports, and, most importantly, reasonable turnaround time.

A great part of studies on the correlation between gene mutations and prognosis in acute myeloid leukemia (AML) patients are based on Western populations. To profile the genomic landscape of AML patients in Northeast China, we retrospectively analyzed the clinical data of 377 newly diagnosed AML patients in Shengjing Hospital of China Medical University from 2016 to 2022 and compared them with data from other populations with different genetic backgrounds. The mutation status of NPM1, FLT3-ITD, FLT3-TKD, CEBPA (CCAT enhancer binding protein alpha), ASXL1, TET2, KIT, DNMT3A (DNA methyltransferase 3A), IDH1, IDH2, EZH2 (enhancer of zeste 2), RUNX1, TP53, NRAS, and GATA2 was acquired by next-generation sequencing (NGS) technology; meanwhile, the clinical data of the patients were collected. The Cox regression model was used to analyze factors affecting patient survival and the impact of CEBPA and DNMT3A mutation on prognosis, and the results were different from those in other populations. Seventy-seven of 377 patients (20.4%) were detected with CEBPA mutations, which was higher than the 2%–6% in the Caucasian population. In the CEBPA^dm patients who did not receive bone marrow transplantation, the prognosis of male patients (n = 18) was significantly better than that of female patients (n = 21) (p = 0.0242). Sixty-three of 377 patients (16.7%) carried the DNMT3A mutation, which was lower than the mutation frequency of 20.9% in the German–Austrian population, and the prognosis of these patients was significantly poorer (p = 0.0052). In addition, the prognostic evaluation value of the DNMT3A mutation in AML patients was not affected regardless of the presence of the NPM1 and FLT3-ITD comutation (p > 0.05), nor the mutation site of DNMT3A. In conclusion, for the Northeastern Chinese population, the prognosis of male patients with CEBPA^dm was more favorable than that of female patients, and the DNMT3A mutation serves as an independent predictor of poor prognosis in AML. These results highlighted the central role of genetic background in precision medicine strategies and further emphasized the importance of the clinical characteristics of AML gene mutations in the Chinese population.

Juvenile polyposis syndrome (JPS) is a rare precancerous condition associated with a high susceptibility to colorectal cancer. The genetic basis of JPS has been reported to lie in germline mutations in BMPR1A or SMAD4, resulting in diverse clinical manifestations and an elusive underlying mechanism. We firstly utilized a 139-gene next-generation sequencing (NGS) panel to detect the germline variants and further employed various prediction tools to assess the pathogenicity and functional alternations. Consequently, we identified a novel pathogenic BMPR1A missense variant (c.355C>T; p.R119C). More importantly, we proposed for the first time that the missense variant would lead to a decrease in molecular weight, potentially associated with reduced protein stability, diminished posttranslational modifications, and aberrant alternative splicing. These findings may provide novel perspectives for further exploration into the role of BMPR1A in JPS development. Also, we hope to encourage clinicians to underscore the importance of genetic testing and analysis in facilitating the diagnosis and treatment of diseases.

Background: The autosomal recessive metabolic disorder hyperostosis–hyperphosphatemia syndrome (HHS) is characterized by hyperphosphatemia, hyperostosis, and recurrent bone lesions. Patients may develop ectopic and vascular calcification and may present diaphyseal pain of the long bones that is misdiagnosed as osteomyelitis. Mutations in GALNT3 and FGF23 genes were detected in patients with HHS. The main manifestations of these patients are increased levels of phosphate reabsorption from kidneys and painful swelling of long bones alongside with normal levels of vitamin D and parathormone.

Method: We performed whole-exome sequencing (WES) in seven Iranian patients. These patients were referred from several specialist clinics. Seven irrelevant families were examined for genetic mutations.

Results: WES revealed the deleterious missense mutation c.471C>A, p. F157L in all affected members of six families. The variant c.1524+1G>A in the GALNT3 gene was found in the remaining patient which is reported previously. These variants were confirmed utilizing segregation studies in the pedigrees.

Conclusion: Our data together with previous studies related to mutations in FGF23 in Iran strongly support that p. F157L mutation is abundantly prevalent in patients with Iranian origin and is likely to be a founder mutation; however, it requires further confirmative study. The result of this study suggests that p. F157L mutation should be investigated at the first step in genetic analysis of patients with HHS. This enables fast and accurate focused molecular diagnosis and would be effective for use in carrier screening as well as in prenatal diagnosis (PND) and preimplantation genetic diagnosis (PGD).

Purpose: The study was aimed at identifying the pathogenic gene responsible for X-linked nonsyndromic hearing loss (NSHL) in a five-generation Chinese family and at elucidating the gene’s function both in vivo using a zebrafish model and in vitro using PRPS1 knockdown HEI-OC1 cells.

Methods: Exome sequencing (ES) and Sanger sequencing were used to identify the pathogenic variants. A transgenic zebrafish model overexpressing the novel PRPS1 variant (c.494G>A: p.Cys165Tyr) was constructed, and PRPS1 was knocked down in HEI-OC1 cells using siRNA to explore the underlying mechanisms. Hair cell development and behavior were assessed in zebrafish, and mitochondrial function and cell viability were analyzed in HEI-OC1 cells.

Results: A novel missense variant (c.494G>A: p.Cys165Tyr) in the PRPS1 gene was identified as the pathogenic variant causing progressive X-linked deafness-1 (DFNX1). The variant led to hair cell death in zebrafish, with disrupted swimming behavior. In HEI-OC1 cells, PRPS1 knockdown resulted in downregulation of the nicotinamide adenine dinucleotide (NAD⁺)/sirtuin 3 (SIRT3)/superoxide dismutase 2 (SOD2) pathway, increased reactive oxygen species (ROS) accumulation, mitochondrial dysfunction, and apoptosis, which were partially rescued by pretreatment with nicotinamide mononucleotide (NMN), a precursor of NAD⁺.

Conclusion: The study reports a novel PRPS1 variant contributing to the variant spectrum of PRPS1 and highlights the role of PRPS1 deficiency in increasing oxidative stress-induced hair cell apoptosis via the NAD⁺/SIRT3/SOD2 pathway. These findings provide new insights into the molecular mechanisms of PRPS1-related hearing loss and potential therapeutic targets.

Genetic factors are estimated to contribute to 80% of people with epilepsy. However, only four genes were reported to be associated with temporal lobe epilepsy (TLE). This study is aimed at investigating the association between ACTB and TLE. Trio-based exome sequencing was performed in a patient, and a de novo ACTB variant was identified. The patient presented with TLE featuring by age of onset in juvenile, seizure-free status in adulthood, complications of memory decline and irritability, epileptic discharges in the bilateral temporal lobes, and bilateral hippocampal sclerosis. The pathogenicity of the identified ACTB variant was supposed by multiple pieces of evidence, including the missense tolerance ratio of 0%, high conservation of the affected residue, predicted to be “damaging” or “conserved” by 17 in silico tools, and classification of likely pathogenic variant by the American College of Medical Genetics and Genomics (ACMG) guidelines. Protein modeling indicated the alteration of protein structure and stability caused by the identified variant. The spatiotemporal expression of ACTB is consistent with the phenotypic features of this patient. This study suggested that ACTB is a novel candidate causative gene of TLE. The correlation between phenotypes and spatial–temporal expression provides a novel perspective for further exploration of the pathogenesis and prognosis of the disease.

Usher syndrome (USH) is a rare genetic disease characterized by sensorineural deafness and blindness called retinitis pigmentosa, and it is inherited in an autosomal recessive pattern with a prevalence of four to 17 per 100,000 people worldwide. In this study, a consanguineous Chinese family with USH, including two affected individuals and five unaffected individuals, was recruited. All subjects received an ophthalmic examination and an auditory examination. The two USH patients exhibited severe early-onset hearing and vision loss. DNA samples from the two USH patients were analyzed using whole-exome sequencing. A novel homozygous frameshift mutation (NM_206933.4:c.6379_6380delinsC, p.G2127Pfs∗25) in USH2A, resulting in a truncated USH2A protein lacking 3051 amino acids, was identified in the proband. In addition, novel compound mutations in USH2A (one allele harboring NM_206933.4:c.9958G>T, p.G3320C; NM_206933.4:c.8284C>G, p.P2762A; and the other NM_206933.4:c.6379_6380delinsC; p.G2127Pfs∗25) were identified in the other affected individual. In silico analysis predicts that while the p.G3320C mutation has little impact on the local structure around the mutation site, the p.P2762A substitution may alter the protein’s interaction with its binding partners. In addition, p.G2127Pfs∗25 causes a truncation of a major portion of the protein that severely disrupts the protein structure and results in the loss of its function. In conclusion, this study identified novel USH mutations in USH2A and expanded the spectrum of disease-associated variants in the USH2A gene, which will promote the molecular screening of genetic mutations in USH patients.

Background: Birt–Hogg–Dubé syndrome (BHD) was an autosomal dominant disorder caused by a mutation in the folliculin (FLCN) gene and characterized by benign cutaneous fibrofolliculomas in the head and neck, pulmonary cysts, spontaneous pneumothorax, and combined renal tumors.

Methods: This study reported a familial case presenting multiple pulmonary bullae, recurrent spontaneous pneumothorax, diffuse cystic lesions in both lungs, and renal cysts. To further clarify the diagnosis, next-generation sequencing (NGS) was performed in conjunction with the clinical diagnostic criteria for Birt–Hogg–Dubé. The eukaryotic recombinant expression vectors of pEGFP-C1-FLCN and knock-in FLCN mutation by CRISPR/Cas9 were conducted in 293 T and BEAS-2B cell lines. The mRNA and protein expression of the FLCN mutation were verified by fluorescence quantitative PCR and Western blot assay. Nonsense-mediated mRNA decay (NMD) assays and immunohistochemical assays were conducted to elucidate the pathogenicity of the mutation and explore potential mechanisms.

Results: A unique, novel, unspecified significance FLCN mutation NM_144997.7: c.21_22del (p. Cys8 Profs ^∗28) in Exon 4 was detected in both patients. The results demonstrated that the newly identified FLCN frameshift mutation significantly decreased FLCN mRNA and protein expression. The NMD complex recognized and degraded mRNAs containing a premature termination codon (PTC) in the open reading frame of the FLCN frameshift mutation, resulting in haploinsufficiency and ultimately contributing to the manifestation of BHD. Protein expression on the AMP-activated protein kinase (AMPK), Wnt/β-catenin, and mammalian target of rapamycin (mTOR) signaling pathways by immunohistochemistry indicated that FLCN frameshift mutations were responsible for BHD through the activation of AMPK, Wnt/β-catenin, and mTOR signaling pathways.

Conclusion: The study demonstrated that a novel FLCN frameshift mutation was responsible for the pathogenesis of BHD and preliminarily demonstrated that FLCN causes BHD through the AMPK, Wnt/β-catenin, and mTOR signaling pathways.

Incontinentia pigmenti (IP) is a rare hereditary disorder affecting 1.2 in 100,000 live births, predominantly females. Genetic analysis of IP is complicated by a homologous pseudogene, making conventional short-read sequencing challenging. While long-range PCR is typically used to overcome this, skewed X-inactivation detection can also aid in assigning variants to IKBKG. We employed a comprehensive approach, incorporating whole-exome sequencing (WES), long-range PCR, RT-PCR, X-inactivation analysis, and nanopore sequencing, to identify and accurately phase a small heterozygous deletion, NM_001099857.5: c.363_367del, p.(Leu122Glyfs ^∗14), in the IKBKG gene in an IP-affected family. The deletion was initially detected via WES, with skewed X-inactivation observed in both the proband and her mother. Long-range PCR specific to IKBKG confirmed the variant’s location in the IKBKG gene, not in the pseudogene. On the RNA level, the variant was undetectable, suggesting nonsense-mediated decay of the transcript. Nanopore sequencing precisely mapped the variant to IKBKG and analyzed the methylation status of both alleles, confirming the skewed X-inactivation, with the variant-carrying allele predominantly inactivated. This demonstrates the nanopore sequencing’s value in genetic diagnosis, enabling precise variant localization and analysis of X chromosome activation status in females with skewed X-inactivation, aiding in accurate diagnosis and understanding of IP.

This study was aimed at assessing the diagnostic utility of whole genome sequence analysis in a well-characterised research cohort of individuals referred with a clinical suspicion of Cornelia de Lange syndrome (CdLS) in whom prior genetic testing had not identified a causative variant. Short-read whole genome sequencing was performed on 195 individuals from 105 families, 108 of whom were affected. 100/108 of the affected individuals had prior relevant genetic testing, with no pathogenic variant being identified. The study group comprised 42 trios in which both parental samples were available for testing (42 affected individuals and 126 unaffected parents), 61 singletons (unrelated affected individuals), and two families with more than one affected individual. The results showed that 32 unrelated probands from 105 families (30.5%) had likely causative coding region-disrupting variants. Four loci were identified in > 1 proband: NIPBL (10), ANKRD11 (6), EP300 (3), and EHMT1 (2). Single variants were detected in the remaining genes (EBF3, KMT2A, MED13L, NLGN3, NR2F1, PHIP, PUF60, SET, SETD5, SMC1A, and TBL1XR1). Possibly causative variants in noncoding regions of NIPBL were identified in four individuals. Single de novo variants were identified in five genes not previously reported to be associated with any developmental disorder: ARID3A, PIK3C3, MCM7, MIS18BP1, and WDR18. The clustering of de novo noncoding variants implicates a single upstream open reading frame (uORF) and a small region in Intron 21 in NIPBL regulation. Causative variants in genes encoding chromatin-associated proteins, with no defined influence on cohesin function, appear to result in CdLS-like clinical features. This study demonstrates the clinical utility of whole genome sequencing as a diagnostic test in individuals presenting with CdLS or CdLS-like phenotypes.