Molecular Genetics & Genomic Medicine最新文献

Background: SOST encodes a secreted glycoprotein that is similar in sequence to the differential screening-selected gene aberrative in neuroblastoma (DAN) family of bone morphogenetic protein (BMP) antagonists. Pathogenic variants in the SOST gene result in sclerosteosis, van Buchem disease (VBD), or craniodiaphyseal dysplasia. SOST-related genetic disorders are very rare, and limited studies have reported variants associated with sclerosteosis.

Methods: Clinical tests such as magnetic resonance imaging (MRI), computed tomography (CT), emission computed tomography (ECT), electromyogram (EMG), routine blood tests, and physical examinations were conducted for the proband. Trio-whole exome sequencing (Trio-WES) was performed, and the rare variants (allele frequency < 0.01) in the exon and splicing regions were selected for further pathogenic evaluation. Candidate pathogenic variants were validated through Sanger sequencing. The wild and mutant SOST sequences were cloned into the pcDNA3.1 expression vector, and the RNA and protein expression levels were investigated in the HEK293T cell line.

Results: In this study, we present a case study of a proband who displays abnormal facial expressions accompanied by numbness. The results of the brain MRI show thickening of the skull and disappearance of the diplopia signal. The temporal bone CT scan indicates diffuse osteosclerosis affecting the bilateral ossicular chains and internal auditory meatus, as well as stenosis of the bilateral internal auditory meatus. Trio-WES sequencing detected a novel homozygous variant in the proband: NM_025237.3(SOST): c.327C>A (p.Cys109*), which was also validated in his sister from the same family. According to the ACMG guidelines, the variant is classified as "likely pathogenic." The in vitro experiments demonstrated that the variant caused a decrease in SOST expression at RNA and protein level and produced a truncated protein.

Conclusion: The report presents new evidence for the clinical diagnosis of SOST-related facial numbness and expands the variant spectrum of SOST.

Background: We identified a novel variant in MBD5 located within intron 6: c.114-13A>G (NM_018328.5) in a family with a patient presenting intellectual disability. This variant is hypothesized to be the etiological agent underlying the patient's condition.

Methods: We conducted an analysis of mRNA splicing within the patient and their relatives' blood samples via reverse transcription polymerase chain reaction (RT-PCR) to assess intronic mRNA splicing. Additionally, we employed a minigene vector construction approach to verify in vitro the splicing of mRNA containing the mutated fragment. Protein structure prediction analysis of the aberrant mRNA was performed using PyMOL software.

Results: The patient harbors a novel mutation in the MBD5 gene: c.114-13A>G. Analysis of the patient's blood sample revealed the presence of aberrantly sized mRNA molecules. Utilizing a minigene approach, we discovered that this mutation results in the generation of two types of abnormally sized mRNAs. The first type of abnormal splicing leads to a 12-base pair retention at the 3' end of intron 6, and the second type of abnormal splicing causes exon 7 skipping.

Conclusion: In accordance with the "Standards and Guidelines for the Interpretation of Sequence Variants" established by the American College of Medical Genetics and Genomics (ACMG), the novel mutation c.114-13A>G in the MBD5 gene meets the criteria for PS2 (the variant is de novo and not inherited from either parent) and PS3 (the variant affects mRNA splicing, resulting in aberrant transcripts). We propose that the c.114-13A>G variant, located within intron 6 of the MBD5 gene, is pathogenic. This discovery not only expands the repository of pathogenic variants for MBD5 but also provides additional insights into intronic mutations of the MBD5 gene, thereby offering significant information for the genetic diagnosis of Autosomal Dominant Intellectual Disability Type 1.

Background: Paired Box 2 (PAX2, NM_000278.5) encodes paired box gene 2, one of many human homologs of the Drosophila melanogaster gene prd. PAX2-related disorder is an autosomal dominant disorder associated with renal and eye abnormalities.

Methods: In this study, both monochorionic diamniotic twins presenting bilateral renal agenesis were subjected to investigation. The pregnancy was terminated and muscular tissue of the fetus was analyzed by trio whole exome sequencing (WES). The target sequence was verified by Sanger sequencing at the genome level. In vitro Minigene model was constructed and the transcribed cDNA was subjected to Sanger sequencing to explore the splicing effect of the suspected mutation.

Results: The synonymous mutation PAX2 c.792G>A was detected in both twins, but not in the parents or the family's firstborn. Although this mutation did not alter the amin acid sequence, minigene splice analysis confirmed that c.792G>A resulted in exon 6 skipping, leading to aberrant mRNA splicing.

Conclusion: PAX2 c.792G>A is the first pathogenic synonymous mutation ever documented. It has a significant impact on mRNA splicing and leads to developmental abnormalities. This case highlights the importance of clinical phenotyping as well as comprehensive genetic analysis during genetic testing, including evaluation of synonymous mutations.

Background: Amelogenesis imperfecta (AI) is a rare genetic disorder causing tooth enamel defects. AI has been classified into 14 different clinical subtypes with different modes of inheritance. In this study, we performed whole-exome sequencing to identify the causative gene defect in a large Dutch family with autosomal dominant hypocalcified AI (ADHCAI).

Methods: Whole-exome sequencing (WES) was performed on genomic DNA of the proband with AI. We focused on eight candidate genes known to be involved in inherited autosomal dominant AI. Sanger sequencing was used to confirm the selected exome candidate variant. Additionally, genotype and phenotype analyses were performed in the selected affected and non-affected individuals and compared according to previously listed literature for this candidate gene of the proband.

Results: The clinical phenotype of the affected individuals showed a generalized and extensive enamel defect of all teeth. In the exome dataset of the proband, a novel nonsense variant in FAM83H, c.1055C>A p.(Ser352*) was detected, which was verified by conventional Sanger sequencing. Co-segregation analysis confirmed that the variant was present in all affected individuals and not in unaffected individuals.

Conclusion: A novel pathogenic, protein-truncating variant was detected in FAM83H, a gene with similar truncating variants known to be associated with ADHCAI.

Introduction: Werner syndrome (WS) is a rare recessive disorder characterized by premature aging and metabolic abnormalities. WS is caused by mutations in the WS RecQ-like helicase gene (WRN), which encodes the WRN RecQ-like helicase protein. This study aimed to identify the deletion mutation in the WRN gene within the WS family and comprehensively analyze its regulatory role.

Methods: We utilized whole exome sequencing to assess gene mutations in non-close relatives of two patients with WS. The mutation was further verified using Sanger sequencing. Subsequently, the pathophysiological characteristics of the mutation were examined using Western blotting, subcellular localization determination, conservative analysis, and three-dimensional (3D) protein structure prediction.

Results: Whole exome sequencing revealed a previously unreported homozygous mutation c.3244delG (p.Val1082Tyrfs*17) within exon 27 of the WRN gene. Sanger sequencing confirmed the presence of a homozygous mutation in the two patients, while a heterozygous mutation was identified in the other six family members. Western blotting revealed that the c.3244delG mutation in the WRN gene resulted in a reduced molecular weight of the mutated WRN protein. Furthermore, subcellular localization experiments revealed that the mutant WRN protein could not be effectively transported to the nucleus. Some studies reported that the mutation exhibits a high conservation rate across various species. The three-dimensional structure prediction indicates that the mutant WRN protein exhibits a distinct structure compared to the wild-type protein.

Conclusions: This study identified a frameshift mutation in the WRN gene, which was associated with WS. The subsequent functional analysis revealed the inefficiency of the mutated protein. This study broadens the spectrum of known WRN mutations and enhances the comprehension of WS pathogenesis.

Background: Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease. However, our current understanding of the genetic etiology for TOF is limited.

Methods: Whole exome sequencing (WES) and Sanger sequencing were applied to a family trio diagnosed with TOF by fetal prenatal ultrasound examination. A minigene assay was performed to confirm the splicing defects.

Results: We identified compound heterozygous variants in the cerebral cavernous malformation 2-like (CCM2L) gene, namely the paternally inherited nonsense variant NM_001365692.1:c.741G>A p.(Trp247Ter) and the maternally inherited splice-site variant NM_001365692.1:c.1263+2T>A in a fetus with TOF featuring a ventricular septal defect associated with overriding aorta and pulmonary stenosis. Minigene assay showed that the c.1263+2T>A variant led to skipping of CCM2L exon8 during RNA splicing, which is thought to result in frameshift and premature termination of translation. Both variants were absent from the public population databases (Genome Aggregation Database [gnomAD], 1000 Genomes [1000G], Clinvar) and classified as likely pathogenic according to the ACMG guidelines (PVS1 + PM2 level evidence).

Conclusion: To our knowledge, this is the first reported case of biallelic loss-of-function variants in human CCM2L. Our findings suggest a potential association of human CCM2L with TOF.

Background: The gastrulation brain homeobox (Gbx) family, including GBX1 and GBX2, is crucial for hindbrain development and contributes to the morphogenesis of the midbrain-hindbrain boundary (MHB). While the role of the GBX1 gene in the development of the human nervous system remains to be elucidated, its variant in humans has not previously been reported to be associated with disease.

Methods: The patient presenting with sleep panic attacks underwent comprehensive clinical assessments, including electroencephalograph (EEG), magnetic resonance imaging (MRI), and genetic testing through whole exome sequencing (WES). Zebrafish models were generated through gbx1 gene crispants to investigate the functional impact of identified genetic variants.

Results: The patient in our study was diagnosed with focal epilepsy through long-range EEG. WES revealed a de novo GBX1 gene variant [NM_001098834.3: c.910C>T (p.Gln304*)]. In zebrafish larvae with gbx1 gene disruption, significant abnormalities were observed in the morphology of the interocular area. Furthermore, these larvae exhibited an increased susceptibility to neurophysiological abnormalities associated with epileptiform activity.

Conclusion: Our study is the first to identify an association between the GBX1 gene variant and focal epilepsy. The zebrafish models confirmed the presence of related phenotypes in the gbx1-Cas9. These findings underscore the significance of the GBX1 gene in neurological function.

Background: Cornelia de Lange syndrome (CdLS) is a rare genetic disorder characterized by congenital multiple anomalies, developmental delay, and distinctive facial features.

Methods: We performed chromosomal microarray analysis (CMA), whole exome sequencing (WES), linked-read whole-genome sequencing (WGS) and optical genome mapping (OGM) to investigate an undiagnosed case of CdLS.

Results: A male patient presented clinical features consistent with CdLS, including a short nose, synophrys, small hands, hearing impairment, refractory complex partial seizures, and developmental delay. Amniocentesis at 28 gestational weeks and karyotyping revealed a presumably balanced translocation between chromosome 5 and chromosome 6. CMA and WES failed to identify copy number variants or a molecular diagnosis. Further analysis using WGS and OGM identified two translocation events on chromosome 5, resulting in three derivative chromosomes: 46,XY, der(2)t(2;5)(q32.3;p13.2),der(5)t(5;6)(p13.1;q12),der(6)t(2;6)(q32.3;q12)ins(6;5)(q12;p13.1p13.2). These rearrangements disrupted the NIPBL gene, a key gene with CdLS, splitting it across derivative chromosomes 2 and 6. Phasing studies revealed that these translocations originated from the paternal lineage.

Conclusions: This case highlights the intricate genetic underpinnings of CdLS in this patient and underscores the diagnostic value of high-resolution genomic analyses in elucidating complex chromosomal rearrangements.

Background: Lenz-Majewski syndrome (LMS) is a rare genetic disorder characterized by osteosclerosis, intellectual disability, characteristic facies, and distinct craniofacial, dental, cutaneous, and distal-limb anomalies. Mutations in the PTDSS1 gene, which encodes one of the phosphatidylserines (PS) synthase enzymes, PSS1, have been identified as causative in LMS patients. These mutations make PSS1 insensitive to feedback inhibition by PS levels.

Methods: Whole genome sequence (WGS) was performed on a patient with congenital cutis laxa and her parents. PS synthase activity was analyzed in PTDSS1 mutant cDNA clones to evaluate functional alterations.

Results: A 5-year-old girl presented with congenital skin wrinkles and was initially diagnosed with congenital cutis laxa. She had bilateral inner ear hypoplasia, bilateral low-frequency hearing loss, attention-deficit/hyperactivity disorder, and mild intellectual disability. Physical examination revealed protruding ears, frontal bossing, and dental malalignment. A de novo heterozygous missense variant in the PTDSS1 gene, c.284G>A (p. Arg95Gln) was identified by WGS. Functional analysis indicated increased PS synthase activity, supporting the pathogenicity of this variant.

Conclusions: The patient's cutis laxa and facial features were consistent with LMS, though radiographic findings did not reveal the characteristic sclerosing bone dysplasia reported in previous cases. This observation suggests that LMS may have a broader phenotypic spectrum than previously recognized.

Background: Pathogenic germline missense and in-frame indel variants in exons 30 or 31 of the EP300 gene are associated with Menke-Hennekam syndrome-2 (MKHK2). The phenotypic spectrum associated with MKHK2 is variable, including neurodevelopmental, respiratory, skeletal, and immunological impairments. Based on their genetic, clinical, and DNA methylation profiles, a recent study proposed three domain-specific subtypes of MKHK: MKHK-ZZ, MKHK-TAZ2, and MKHK-ID4. In somatic cells, EP300 variants have been reported in lymphoma, leukemia, and various solid tumors. We present an African American girl with global developmental delay, failure to thrive, microcephaly, seizure, osteopenia, and T-cell acute lymphoblastic leukemia (T-ALL).

Method: We performed karyotype, FISH, chromosomal microarray, and exome sequencing with probands bone marrow, blood, and buccal swab.

Result: Comprehensive genetic studies using multiple tissues detected somatic complex cytogenomic changes in blood cells and a de novo germline missense variant (NM_001429.4: c.5258G>A, p.Cys1753Tyr) in the TAZ2 domain of EP300 from her buccal swab, which is consistent with a diagnosis of MKHK2. While in our patient we observed phenotypic overlaps with affected individuals harboring variants in the TAZ2 domain, some phenotypes such as osteopenia and alopecia have not been reported previously. The hematolymphoid malignancy of our patient also raises the question of whether germline EP300 variants are associated with a genetic predisposition to cancer.

Conclusion: Together, this case expands the growing body of knowledge regarding the clinical and genetic spectrum of MKHK2. This is the first MKHK individual reported in the literature in an underrepresented population of African American ancestry.