scholarly journals A novel synonymous ABCA3 variant identified in a Chinese family with lethal neonatal respiratory failure

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Weifeng Zhang ◽  
Zhiyong Liu ◽  
Yiming Lin ◽  
Ruiquan Wang ◽  
Jinglin Xu ◽  
...  
Keyword(s):  
Respiratory Failure ◽  
Splice Site ◽  
Pulmonary Surfactant ◽  
Sanger Sequencing ◽  
Monozygotic Twin ◽  
Splice Donor Site ◽  
Patient Specific ◽  
Chinese Family ◽  
Twin Sister ◽  
Synonymous Variant

Abstract Background Lethal respiratory failure is primarily caused by a deficiency of pulmonary surfactant, and is the main cause of neonatal death among preterm infants. Pulmonary surfactant metabolism dysfunction caused by variants in the ABCA3 gene is a rare disease with very poor prognosis. Currently, the mechanisms associated with some ABCA3 variants have been determined, including protein mistrafficking and impaired phospholipid transport. However, some novel variants and their underlying pathogenesis has not been fully elucidated yet. In this study we aimed to identify the genetic features in a family with lethal respiratory failure. Methods We studied members of two generations of a Chinese family, including a female proband, her parents, her monozygotic twin sister, and her older sister. Trio whole exome sequencing (WES) were used on the proband and her parents to identify the ABCA3 variants. Sanger sequencing and real-time quantitative polymerase chain reaction (PCR) were used on the monozygotic twin sister of proband to validate the ABCA3 synonymous variant and exon deletion, respectively. The potential pathogenicity of the identified synonymous variant was predicted using the splice site algorithms dbscSNV11_AdaBoost, dbscSNV11_RandomForest, and Human Splicing Finder (HSF). Results All patients showed severe respiratory distress, which could not be relieved by mechanical ventilation, supplementation of surfactant, or steroid therapy, and died at an early age. WES analysis revealed that the proband had compound heterozygous ABCA3 variants, including a novel synonymous variant c.G873A (p.Lys291Lys) in exon 8 inherited from the mother, and a heterozygous deletion of exons 4–7 inherited from the father. The synonymous variant was consistently predicted to be a cryptic splice donor site that may lead to aberrant splicing of the pre-mRNA by three different splice site algorithms. The deletion of exons 4–7 of the ABCA3 gene was determined to be a likely pathogenic variant. The variants were confirmed in the monozygotic twin sister of proband by Sanger sequencing and qPCR respectively. The older sister of proband was not available to determine if she also carried both ABCA3 variants, but it is highly likely based on her clinical course. Conclusions We identified a novel synonymous variant and a deletion in the ABCA3 gene that may be responsible for the pathogenesis in patients in this family. These results add to the known mutational spectrum of the ABCA3 gene. The study of ABCA3 variants may be helpful for the implementation of patient-specific therapies.

scholarly journals A novel synonymous ABCA3 variant identified in a Chinese family with lethal neonatal respiratory failure

2021 ◽  
Author(s):  
Weifeng Zhang ◽  
Zhiyong Liu ◽  
Yiming Lin ◽  
Ruiquan Wang ◽  
Jinglin Xu ◽  
...  
Keyword(s):  
Respiratory Failure ◽  
Splice Site ◽  
Quantitative Polymerase Chain Reaction ◽  
Donor Site ◽  
Splice Donor Site ◽  
Patient Specific ◽  
Chinese Family ◽  
Compound Heterozygous ◽  
Loss Of Function ◽  
Synonymous Variant

Abstract Background: Lethal respiratory failure is mostly caused by pulmonary surfactant (PS) deficiency and is the main cause of neonatal death. PS metabolism dysfunction caused by mutations in the ABCA3 gene is a rare disease with very poor prognosis. However, the underlying mechanism of genetic mutations causing PS metabolism dysfunction has not been fully elucidated yet. This study aimed to identify the genetic features in a family with lethal respiratory failure.Methods: We studied members of a two-generation Chinese family including a female proband, her parents, her identical twin sister, and her older sister. Whole exome sequencing (WES), Sanger sequencing, and real-time quantitative polymerase chain reaction （PCR） were used to identify and validate the ABCA3 mutation. The potential pathogenicity of the identified synonymous variant was predicted using splice site algorithms (dbscSNV11_AdaBoost, dbscSNV11_RandomForest, and HSF).Results: All patients showed severe respiratory distress, which could not be relieved by mechanical ventilation, supplementation of surfactants, or steroid therapy, and died at an early age. Molecular genetic analysis revealed that the patients had compound heterozygous ABCA3 variants, including a novel synonymous variant c.G873A (p.Lys291Lys) in exon 8 derived from the mother and a heterozygous deletion of exons 4-7 derived from the father. The synonymous variant was consistently predicted to be a cryptic splice donor site that may lead to aberrant splicing of the pre-mRNA by three different splice site algorithms. The deletion of exons 4-7 of the ABCA3 gene was determined to be a loss-of-function pathogenic variant.Conclusions: We identified a novel synonymous variant and a deletion in the ABCA3 gene that may be responsible for the pathogenesis in patients in this family. These results enrich the known mutational spectrum of the ABCA3 gene. Moreover, the study of ABCA3 mutations is helpful for the realization of patient-specific therapies.

scholarly journals A Novel Homozygous VPS13B Splice-Site Mutation Causing the Skipping of Exon 38 in a Chinese Family With Cohen Syndrome

2021 ◽  
Vol 9 ◽  
Author(s):  
Liangshan Li ◽  
Xiangmao Bu ◽  
Yuhua Ji ◽  
Ping Tan ◽  
Shiguo Liu
Keyword(s):  
Splice Site ◽  
Reverse Transcription ◽  
Sanger Sequencing ◽  
Splice Site Mutation ◽  
Chinese Family ◽  
Sequencing Analysis ◽  
Site Mutation ◽  
Transcription Analysis ◽  
Cohen Syndrome ◽  
The Impact

Background: Cohen syndrome (CS) is a clinically heterogeneous disorder characterized by extensive phenotypic variation with autosomal recessive inheritance. VPS13B was identified to be the disease-causing gene for CS. The objectives of the present study were to screen likely pathogenic mutations of the patient with developmental delay and mental retardation, and to determinate the effect of this splice-site mutation by reverse transcription analysis.Methods: Whole exome sequencing (WES) in combination with Sanger sequencing were performed to identify the causative mutations of this CS family. Subsequently, the impact of the intronic variant on splicing was analyzed by reverse transcription and the construction of expression vector.Results: A novel homozygous splice-site mutation (c.6940+1G>T) in the VPS13B gene was identified in this proband. Sanger sequencing analysis of the cDNA demonstrated that the c.6940+1G>T variant could cause the skipping of entire exon 38, resulting in the loss of 208 nucleotides and further give rise to the generation of a premature in-frame stop codon at code 2,247.Conclusions: The homozygous VPS13B splicing variant c.6940+1G>T was co-segregated with the CS phenotypes in this family and was identified to be the cause of CS after comprehensive consideration of the clinical manifestations, genetic analysis and cDNA sequencing result.

scholarly journals A rare large duplication of MLH1 identified in Lynch syndrome

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Abhishek Kumar ◽  
Nagarajan Paramasivam ◽  
Obul Reddy Bandapalli ◽  
Matthias Schlesner ◽  
Tianhui Chen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Lynch Syndrome ◽  
Splice Site ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Splice Donor Site ◽  
Laboratory Diagnostics ◽  
Mmr Genes ◽  
Base Pair Deletion ◽  
Splice Site Variant

Abstract Background The most frequently identified strong cancer predisposition mutations for colorectal cancer (CRC) are those in the mismatch repair (MMR) genes in Lynch syndrome. Laboratory diagnostics include testing tumors for immunohistochemical staining (IHC) of the Lynch syndrome-associated DNA MMR proteins and/or for microsatellite instability (MSI) followed by sequencing or other techniques, such as denaturing high performance liquid chromatography (DHPLC), to identify the mutation. Methods In an ongoing project focusing on finding Mendelian cancer syndromes we applied whole-exome/whole-genome sequencing (WES/WGS) to 19 CRC families. Results Three families were identified with a pathogenic/likely pathogenic germline variant in a MMR gene that had previously tested negative in DHPLC gene variant screening. All families had a history of CRC in several family members across multiple generations. Tumor analysis showed loss of the MMR protein IHC staining corresponding to the mutated genes, as well as MSI. In family A, a structural variant, a duplication of exons 4 to 13, was identified in MLH1. The duplication was predicted to lead to a frameshift at amino acid 520 and a premature stop codon at amino acid 539. In family B, a 1 base pair deletion was found in MLH1, resulting in a frameshift and a stop codon at amino acid 491. In family C, we identified a splice site variant in MSH2, which was predicted to lead loss of a splice donor site. Conclusions We identified altogether three pathogenic/likely pathogenic variants in the MMR genes in three of the 19 sequenced families. The MLH1 variants, a duplication of exons 4 to 13 and a frameshift variant, were novel, based on the InSiGHT and ClinVar databases; the MSH2 splice site variant was reported by a single submitter in ClinVar. As a variant class, duplications have rarely been reported in the MMR gene literature, particularly those covering several exons.

scholarly journals A 5′ splice site mutation affecting the pre-mRNA splicing of two upstream exons in the collagen COL1A1 gene. Exon 8 skipping and altered definition of exon 7 generates truncated proα1(I) chains with a non-collagenous insertion destabilizing the triple helix

1994 ◽  
Vol 302 (3) ◽  
pp. 729-735 ◽  
Author(s):  
J F Bateman ◽  
D Chan ◽  
I Moeller ◽  
M Hannagan ◽  
W G Cole
Keyword(s):  
Splice Site ◽  
De Novo ◽  
Donor Site ◽  
Mrna Splicing ◽  
Splice Donor Site ◽  
Sequence Motif ◽  
Type I ◽  
Splice Donor ◽  
Site Mutation ◽  
Definition Of

A heterozygous de novo G to A point mutation in intron 8 at the +5 position of the splice donor site of the gene for the pro alpha 1(I) chain of type I procollagen, COL1A1, was defined in a patient with type IV osteogenesis imperfecta. The splice donor site mutation resulted not only in the skipping of the upstream exon 8 but also unexpectedly had the secondary effect of activating a cryptic splice site in the next upstream intron, intron 7, leading to re-definition of the 3′ limit of exon 7. These pre-mRNA splicing aberrations cause the deletion of exon 8 sequences from the mature mRNA and the inclusion of 96 bp of intron 7 sequence. Since the mis-splicing of the mutant allele product resulted in the maintenance of the correct codon reading frame, the resultant pro alpha 1(I) chain contained a short non-collagenous 32-amino-acid sequence insertion within the repetitive Gly-Xaa-Yaa collagen sequence motif. At the protein level, the mutant alpha 1(I) chain was revealed by digestion with pepsin, which cleaved the mutant procollagen within the protease-sensitive non-collagenous insertion, producing a truncated alpha 1(I). This protease sensitivity demonstrated the structural distortion to the helical structure caused by the insertion. In long-term culture with ascorbic acid, which stimulates the formation of a mature crosslinked collagen matrix, and in tissues, there was no evidence of the mutant chain, suggesting that during matrix formation the mutant chain was unable to stably incorporated into the matrix and was degraded proteolytically.

scholarly journals Striking Cardiac Phenotypic Variability in A Chinese Family With A MYH7 Splice Site Mutation

2021 ◽  
Author(s):  
Peng Tu ◽  
Hairui Sun ◽  
Xiaohang Zhang ◽  
Qian Ran ◽  
suzhen Ran ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Splice Site ◽  
Phenotypic Variability ◽  
Splice Site Mutation ◽  
Left Ventricular ◽  
Chinese Family ◽  
Site Mutation ◽  
Cardiac Phenotype ◽  
Whole Exome

Abstract Background: Left ventricular non-compaction cardiomyopathy (LVNC) is a rare congenital heart defect (CHD), genetics defects have been found in patients with LVNC and their family members; and MYH7 is the most common genetic associated with LVNC. Methods: A trio (fetus and the parents) whole-exome sequencing (WES) was performed when the fetus was found with Ebstein's anomaly (EA), heart dilatation, perimembranous ventricular septal defects (VSD), mild seroperitoneum and single umbilical artery (SUA).Results: Whole-exome sequencing identified a maternal inherited heterozygous splice site mutation in MYH7 (NM_000257.3:c.732+1G>A). Subsequent Sanger sequencing confirmed that the mutation was heterozygous in the fetus, the old sister, the grandmother, and the mother. QPCR experiment using RNA from blood lymphocytes but were unable to amplify any product.Conclusion: This familial case underlines that the striking cardiac phenotypic of MYH7 mutation (the c.732+1G>A spice site variant) may be highly variable. The mechanistic studies which could uncover candidate genes modulating cardiac phenotype associated with LVNC/EA should be proceed.

scholarly journals A Deep Exon Cryptic Splice Site Promotes Aberrant Intron Retention in a Von Willebrand Disease Patient

2021 ◽  
Vol 22 (24) ◽  
pp. 13248
Author(s):  
John G. Conboy
Keyword(s):  
Secondary Structure ◽  
Splice Site ◽  
Intron Retention ◽  
Donor Site ◽  
Von Willebrand Disease ◽  
Splice Donor Site ◽  
Cryptic Splice Site ◽  
Splice Donor ◽  
Nucleotide Mutation ◽  
Von Willebrand

A translationally silent single nucleotide mutation in exon 44 (E44) of the von Willebrand factor (VWF) gene is associated with inefficient removal of intron 44 in a von Willebrand disease (VWD) patient. This intron retention (IR) event was previously attributed to reordered E44 secondary structure that sequesters the normal splice donor site. We propose an alternative mechanism: the mutation introduces a cryptic splice donor site that interferes with the function of the annotated site to favor IR. We evaluated both models using minigene splicing reporters engineered to vary in secondary structure and/or cryptic splice site content. Analysis of splicing efficiency in transfected K562 cells suggested that the mutation-generated cryptic splice site in E44 was sufficient to induce substantial IR. Mutations predicted to vary secondary structure at the annotated site also had modest effects on IR and shifted the balance of residual splicing between the cryptic site and annotated site, supporting competition among the sites. Further studies demonstrated that introduction of cryptic splice donor motifs at other positions in E44 did not promote IR, indicating that interference with the annotated site is context dependent. We conclude that mutant deep exon splice sites can interfere with proper splicing by inducing IR.

Mutation of COL2A1 in a Chinese Family with Presentations of Legg-Calvé-Perthes Disease

2020 ◽  
Author(s):  
denglu yan ◽  
zhaojie Wang ◽  
Zhi Zhang
Keyword(s):  
Femoral Head ◽  
Sanger Sequencing ◽  
Structural Changes ◽  
Genetic Factors ◽  
Mutation Detection ◽  
Perthes Disease ◽  
Chinese Family ◽  
Col2a1 Gene ◽  
Whole Exome ◽  
Missense Substitution

Abstract Background: The aim of this study was to identify genetic factors and chromosomal regions contributing to osteonecrosis of the femoral head (ONFH) in a Chinese family with presentations of Legg-Calvé-Perthes Disease (LCDP). Methods: In this study, we performed whole exon sequencing of a Chinese family with LCPD for mutation detection. Ten members had ONFH in twenty-seven family members in four generations family, 5 unaffected members of the studied family and 5 normal peoples as control were underwent whole exome sequencing for mutation detection. Structural modeling test was applied to analyze the potential structural changes caused by the missense substitution. Results: In this Chinese family affected by LCPD, the mutation (c.3508 G>A, p. Gly1170Ser) in exon 50 of COL2A1 in the Gly–X–Y domain was present in 10 patients but absent in 5 unaffected members of the studied family and in 5 control chromosomes from unaffected individuals of matched geographical ancestry. The COL2A1 gene mutation was further validated by Sanger sequencing, confirmed that were heterozygous for the mutation. Then, we identified the p.Gly1170Ser mutation in exon 50 of COL2A1 in a Chinese family with LCPD. Conclusions: This study maps the mutation of mutation (c.3508 G>A, p. Gly1170Ser) in exon 50 of COL2A1 in the Gly–X–Y domain in a Chinese family of LCPD, which causes osteonecrosis of femoral head.

scholarly journals A Turkish Female Twin Sister Patient with Fibular Aplasia, Congenital Tibia Pseudoarthrosis, Oligosyndactyly, and Negative WNT7A Gene Mutation

2018 ◽  
Vol 08 (02) ◽  
pp. 095-099
Author(s):  
Hale Önder Yılmaz ◽  
Duran Topak ◽  
Orkun Yılmaz ◽  
Seda Çakmaklı
Keyword(s):  
Case Report ◽  
Clinical Case ◽  
Monozygotic Twin ◽  
Radiographic Examination ◽  
Significant Finding ◽  
Left Tibia ◽  
Twin Sister ◽  
Limb Defect ◽  
Pes Equinovarus ◽  
Normal Twin

AbstractWe report a rare limb defect named as fibular aplasia, tibial campomelia, and oligosyndactyly (FATCO) syndrome in a female monozygotic twin with a normal twin sister, presented with anterior tibia pseudarthrosis, oligosyndactyly, and pes equinovarus. Radiographic examination displayed the absence of left fibulae, anterolateral pseudarthrosis of left tibia, and the absence of some metatarsus and phalangeal bones. Our case report is the first to report that only one of the identical twins was affected by FATCO syndrome, which is a significant finding because the pathogenicity of FATCO syndrome is yet to be identified, and this clinical case may provide a new insight for discovering the etiology of FATCO syndrome.

A novel splice‐site mutation in the A TP2C1 gene of a Chinese family with Hailey‐Hailey disease

2018 ◽  
Vol 120 (3) ◽  
pp. 3630-3636 ◽  
Author(s):  
Heng Xiao ◽  
Xiangjun Huang ◽  
Hongbo Xu ◽  
Xiang Chen ◽  
Wei Xiong ◽  
...  
Keyword(s):  
Splice Site ◽  
Splice Site Mutation ◽  
Chinese Family ◽  
Site Mutation
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