scholarly journals Case Report: A Novel Variant c.2262+3A>T of the SCN5A Gene Results in Intron Retention Associated With Incessant Ventricular Tachycardias

2021 ◽  
Vol 8 ◽  
Author(s):  
Jie Yin ◽  
Jia Zhou ◽  
Jinlong Chen ◽  
Ting Xu ◽  
Zhongman Zhang ◽  
...  
Keyword(s):  
Cardiac Electrophysiology ◽  
Splice Variants ◽  
Stop Codon ◽  
Clinical Manifestations ◽  
Premature Stop Codon ◽  
Splice Donor Site ◽  
Molecular Defect ◽  
Truncated Protein ◽  
Mutant Transcript ◽  
Ventricular Tachycardias

Objective: Voltage-gated sodium channel Nav1.5 encoded by the SCN5A gene plays crucial roles in cardiac electrophysiology. Previous genetic studies have shown that mutations in SCN5A are associated with multiple inherited cardiac arrhythmias. Here, we investigated the molecular defect in a Chinese boy with clinical manifestations of arrhythmias.Methods: Gene variations were screened using whole-exome sequencing and validated by direct Sanger sequencing. A minigene assay and reverse transcription PCR (RT-PCR) were performed to confirm the effects of splice variants in vitro. Western blot analysis was carried out to determine whether the c.2262+3A>T variant produced a truncated protein.Results: By genetic analysis, we identified a novel splice variant c.2262+3A>T in SCN5A gene in a Chinese boy with incessant ventricular tachycardias (VT). This variant was predicted to activate a new cryptic splice donor site and was identified by in silico analysis. The variant retained 79 bp at the 5′ end of intron 14 in the mature mRNA. Furthermore, the mutant transcript that created a premature stop codon at 818 amino acids [p.(R818*)] could be produced as a truncated protein.Conclusion: We verified the pathogenic effect of splicing variant c.2262+3A>T, which disturbed the normal mRNA splicing and caused a truncated protein, suggesting that splice variants play an important role in the molecular basis of early onset incessant ventricular tachycardias, and careful molecular profiling of these patients will be essential for future effective personalized treatment options.

scholarly journals Type I Glanzmann thrombasthenia caused by an apparently silent β3 mutation that results in aberrant splicing and reduced β3 mRNA

2005 ◽  
Vol 93 (05) ◽  
pp. 897-903 ◽  
Author(s):  
Jingli Xie ◽  
Dina Pabón ◽  
Asier Jayo ◽  
Nora Butta ◽  
Consuelo González-Manchón
Keyword(s):  
Genomic Dna ◽  
Stop Codon ◽  
Genetic Defect ◽  
Premature Stop Codon ◽  
Splice Donor Site ◽  
Type I ◽  
Glanzmann Thrombasthenia ◽  
Base Pair Deletion ◽  
Mutant Transcript ◽  
Exon 11

SummaryWe report a novel genetic defect in a patient with type I Glanzmann thrombasthenia. Flow cytometry analysis revealed undetectable levels of platelet glycoproteins αIIb and β3, although residual amounts of both proteins were detectable in immunoblotting analysis. Sequence analysis of reversely transcribed platelet β3 mRNA showed a 100-base pair deletion in the 3’-boundary of exon 11, that results in a frame shift and appearance of a premature STOP codon. Analysis of the corresponding genomic DNA fragment revealed the presence of a homozygous C1815T transition in exon 11. The mutation does not change the amino acid residue but it creates an ectopic consensus splice donor site that is used preferentially, causing splicing out of part of exon 11. The parents of the proband, heterozygous for this mutation, were asymptomatic and had reduced platelet content of αIIbβ3. PCR-based relative quantification of β3 mRNA failed to detect the mutant transcript in the parents and showed a marked reduction in the patient. The results suggest that the thrombasthenic phenotype is, mainly, the result of the reduced availability of β3-mRNA, most probably due to activation of the nonsense-mediated mRNA decay mechanism. They also show the convenience of analyzing both genomic DNA and mRNA, in order to ascertain the functional consequences of single nucleotide substitutions.

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 novel nonsense PTH1R variant shows incomplete penetrance of primary failure of eruption: a case report

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Cristina Grippaudo ◽  
Concetta Cafiero ◽  
Isabella D’Apolito ◽  
Agnese Re ◽  
Maurizio Genuardi ◽  
...  
Keyword(s):  
Stop Codon ◽  
Clinical Manifestations ◽  
Premature Stop Codon ◽  
Diagnostic Value ◽  
Open Bite ◽  
Incomplete Penetrance ◽  
Functional Protein ◽  
Case Presentation ◽  
Primary Failure Of Eruption ◽  
Buccal Swabs

Abstract Background Aim of this work was to describe a rare inheritance pattern of Primary Failure of Eruption (PFE) in a small family with incomplete penetrance of PFE and a novel nonsense PTH1R variant. Case presentation The proband, a 26 year-old man with a significant bilateral open-bite, was diagnosed with PFE using clinical and radiographic characteristics. DNA was extracted from the proband and his immediate family using buccal swabs and the entire PTH1R coding sequence was analyzed, revealing a novel heterozygous nonsense variant in exon 7 of PTH1R (c.505G > T). This variant introduces a premature stop codon in position 169, predicted to result in the production of a truncated and non-functional protein. This variant has never been reported in association with PFE and is not present in the Genome Aggregation Database (gnomAD). Interestingly, the c.505G > T variant has also been identified in the unaffected mother of our proband, suggesting incomplete penetrance of PFE. Conclusions In this study, we report a new PTH1R variant that segregates in an autosomal dominant pattern and causes PFE with incomplete penetrance. This underlines the diagnostic value of a thorough clinical and genetic analysis of all family members in order to estimate accurate recurrence risks, identify subtle clinical manifestations and provide proper management of PFE patients.

scholarly journals Interferon lambda 4 expression is suppressed by the host during viral infection

2016 ◽  
Vol 213 (12) ◽  
pp. 2539-2552 ◽  
Author(s):  
MeeAe Hong ◽  
Johannes Schwerk ◽  
Chrissie Lim ◽  
Alison Kell ◽  
Abigail Jarret ◽  
...  
Keyword(s):  
Biochemical Characterization ◽  
Splice Variants ◽  
Stop Codon ◽  
Association Studies ◽  
Premature Stop Codon ◽  
Genetic Association Studies ◽  
Protein Isoforms ◽  
Translation Efficiency ◽  
Regulation Of Expression ◽  
Protein Coding

Interferon (IFN) lambdas are critical antiviral effectors in hepatic and mucosal infections. Although IFNλ1, IFNλ2, and IFNλ3 act antiviral, genetic association studies have shown that expression of the recently discovered IFNL4 is detrimental to hepatitis C virus (HCV) infection through a yet unknown mechanism. Intriguingly, human IFNL4 harbors a genetic variant that introduces a premature stop codon. We performed a molecular and biochemical characterization of IFNλ4 to determine its role and regulation of expression. We found that IFNλ4 exhibits similar antiviral activity to IFNλ3 without negatively affecting antiviral IFN activity or cell survival. We show that humans deploy several mechanisms to limit expression of functional IFNλ4 through noncoding splice variants and nonfunctional protein isoforms. Furthermore, protein-coding IFNL4 mRNA are not loaded onto polyribosomes and lack a strong polyadenylation signal, resulting in poor translation efficiency. This study provides mechanistic evidence that humans suppress IFNλ4 expression, suggesting that immune function is dependent on other IFNL family members.

scholarly journals Band 3 Campinas: A Novel Splicing Mutation in the Band 3 Gene (AE1 ) Associated With Hereditary Spherocytosis, Hyperactivity of Na+/Li+ Countertransport and an Abnormal Renal Bicarbonate Handling

Blood ◽  
1997 ◽  
Vol 90 (7) ◽  
pp. 2810-2818 ◽  
Author(s):  
Paulo R.M. Lima ◽  
José A.R. Gontijo ◽  
José B. Lopes de Faria ◽  
Fernando F. Costa ◽  
Sara T.O. Saad
Keyword(s):  
Hereditary Spherocytosis ◽  
Stop Codon ◽  
Collecting Duct ◽  
Direct Sequencing ◽  
Donor Site ◽  
Premature Stop Codon ◽  
Band 3 ◽  
Base Substitution ◽  
Molecular Defect ◽  
Urinary Acidification

Abstract We have studied the molecular defect underlying band 3 deficiency in one family with hereditary spherocytosis using nonradioactive single strand conformation polimorphism of polymerase chain reaction (PCR) amplified genomic DNA of the AE1 gene. By direct sequencing, a single base substitution in the splicing donor site of intron 8 (position + 1G → T) was identified. The study of the cDNA showed a skipping of exon 8. This exon skipping event is responsible for a frameshift leading to a premature stop codon 13 amino acids downstream. The distal urinary acidification test by furosemide was performed to verify the consequences of the band 3 deficiency in α intercalated cortical collecting duct cells (αICCDC). We found an increased basal urinary bicarbonate excretion, associated with an increased basal urinary pH and an efficient distal urinary acidification. We also tested the consequences of band 3 deficiency on the Na+/H+ exchanger, by the measurement of Na+/Li+ countertransport activity in red blood cells. The Na+/Li+ countertransport activity was increased threefold to sixfold in the patients compared with the controls. It is possible that band 3 deficiency in the kidney leads to a decrease in the reabsorption of HCO−3 in αICCDC and anion loss, which might be associated with an increased sodium-lithium countertransport activity.

scholarly journals Intronic splicing of hyaluronan synthase 1 (HAS1): a biologically relevant indicator of poor outcome in multiple myeloma

Blood ◽  
2005 ◽  
Vol 105 (12) ◽  
pp. 4836-4844 ◽  
Author(s):  
Sophia Adamia ◽  
Tony Reiman ◽  
Mary Crainie ◽  
Michael J. Mant ◽  
Andrew R. Belch ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Monoclonal Gammopathy ◽  
Splice Variants ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Hyaluronan Synthase ◽  
Gene Splicing ◽  
Biologically Relevant ◽  
Mitotic Abnormalities ◽  
The Family

Abstract In this study, we show that the hyaluronan synthase 1 (HAS1) gene undergoes aberrant intronic splicing in multiple myeloma (MM). In addition to HAS1 full length (HAS1FL), we identify 3 novel splice variants of HAS1, HAS1Va, HAS1Vb, and HAS1Vc, detected in patients with MM or monoclonal gammopathy of undetermined significance (MGUS). HAS1Vb and HAS1Vc undergo intronic splicing with creation of a premature stop codon. MM cells expressing one or more HAS1 variants synthesize extracellular and/or intracellular hyaluronan (HA). Expression of the HAS1Vb splice variant was significantly correlated with reduced survival (P = .001). Together, alternative HAS1 gene splicing, the correlations between HAS1 splicing and HA synthesis, and the correlations between HAS1 splicing and reduced survival of MM patients support the hypothesis that the family of HAS1 protein plays a significant role in disease progression. Further, expression of HAS1Vb, in conjunction with HAS1FL and/or other HAS1 variants, may lead to accumulation of intracellular HA molecules and an impact on receptor for HA-mediated motility (RHAMM)-mediated mitotic abnormalities in MM. This study highlights the potential importance of HAS1 and its alternative splicing in pathophysiology of MGUS and MM. (Blood. 2005;105: 4836-4844)

A new ferrochelatase mutation combined with low expression alleles in a Japanese patient with erythropoietic protoporphyria

2002 ◽  
Vol 102 (5) ◽  
pp. 501-506 ◽  
Author(s):  
Yumiko YASUI ◽  
Shikibu MURANAKA ◽  
Tsuyoshi TAHARA ◽  
Ryo SHIMIZU ◽  
Sonoko WATANABE ◽  
...  
Keyword(s):  
Base Pair ◽  
Japanese Patient ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Amino Acid Position ◽  
Molecular Defect ◽  
Wild Type ◽  
Erythropoietic Protoporphyria ◽  
Base Pair Deletion ◽  
Low Expression

We investigated the molecular defect of the ferrochelatase gene in a Japanese patient with erythropoietic protoporphyria (EPP), and identified a novel 16 base pair (574-589) deletion within exon 5. This deletion resulted in a frame-shift mutation and created a premature stop codon at amino acid position 198. The same molecular defect was also identified in his mother and a brother who had symptomatic EPP, but not in his father who was asymptomatic. The subjects with EPP were homozygous for the low expression haplotype, while his father was heterozygous for this haplotype. These results indicate that the combination of a 16 base pair deletion and low expression of the wild-type allelic variant is responsible for EPP in this pedigree.

scholarly journals Resistance to Infection by Subgroups B, D, and E Avian Sarcoma and Leukosis Viruses Is Explained by a Premature Stop Codon within a Resistance Allele of the tvb Receptor Gene

2002 ◽  
Vol 76 (15) ◽  
pp. 7918-7921 ◽  
Author(s):  
Sara Klucking ◽  
Heather B. Adkins ◽  
John A. T. Young
Keyword(s):  
Stop Codon ◽  
Receptor Gene ◽  
Premature Stop Codon ◽  
Resistance Allele ◽  
Truncated Protein ◽  
Single Base ◽  
Single Base Pair ◽  
Resistance To Infection ◽  
Avian Sarcoma

ABSTRACT Here we present the first molecular characterization of the defect associated with an avian sarcoma and leukosis virus (ASLV) receptor resistance allele, tvb r. We show that resistance to infection by subgroups B, D, and E ASLV is explained by the presence of a single base pair mutation that distinguishes this allele from tvb s1, an allele which encodes a receptor for all three viral subgroups. This mutation generates an in-frame stop codon that is predicted to lead to the production of a severely truncated protein.

scholarly journals Evolution of the human gastrokine locus and confounding factors regarding the pseudogenicity of GKN3

2013 ◽  
Vol 45 (15) ◽  
pp. 667-683 ◽  
Author(s):  
Jessica H. Geahlen ◽  
Carlo Lapid ◽  
Kaisa Thorell ◽  
Igor Nikolskiy ◽  
Won Jae Huh ◽  
...  
Keyword(s):  
Selective Sweep ◽  
Stop Codon ◽  
Genetic Locus ◽  
Donor Site ◽  
Premature Stop Codon ◽  
Population Based ◽  
Splice Donor Site ◽  
Human Populations ◽  
Selective Sweeps ◽  
Gastric Mucous

In a screen for genes expressed specifically in gastric mucous neck cells, we identified GKN3, the recently discovered third member of the gastrokine family. We present confirmatory mouse data and novel porcine data showing that mouse GKN3 expression is confined to mucous cells of the corpus neck and antrum base and is prominently expressed in metaplastic lesions. GKN3 was proposed originally to be expressed in some human populations and a pseudogene in others. To investigate that hypothesis, we studied human GKN3 evolution in the context of its paralogous genomic neighbors, GKN1 and GKN2. Haplotype analysis revealed that GKN3 mimics GKN2 in patterns of exonic SNP allocation, whereas GKN1 appeared to be more stringently selected. GKN3 showed signatures of both directional selection and population based selective sweeps in humans. One such selective sweep includes SNP rs10187256, originally identified as an ancestral tryptophan to premature STOP codon mutation. The derived (nonancestral) allele went to fixation in Asia. We show that another SNP, rs75578132, identified 5 bp downstream of rs10187256, exhibits a second selective sweep in almost all Europeans, some Latinos, and some Africans, possibly resulting from a reintroduction of European genes during African colonization. Finally, we identify a mutation that would destroy the splice donor site in the putative exon3-intron3 boundary, which occurs in all human genomes examined to date. Our results highlight a stomach-specific human genetic locus, which has undergone various selective sweeps across European, Asian, and African populations and thus reflects geographic and ethnic patterns in genome evolution.

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