Nucleotide Of Exon Research Articles

The novel HLA-B*15:644 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-B*15:644 differs from HLA-B*15:17:01:02 by one nucleotide in exon 4.

The novel HLA-C*01:02:89 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-C*01:02:89 differs from HLA-C*01:02:01:01 by one nucleotide in exon 2.

The novel HLA-DQB1*04:93 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-DQB1*04:93 differs from HLA-DQB1*04:01:01:01 by one nucleotide in exon 2.

Aberrant splicing caused by exonic single nucleotide variants positioned 2nd or 3rd to the last nucleotide in the COL4A5 gene

Background and objectivesThe evident genotype–phenotype correlation shown by the X-linked Alport syndrome warrants the assessment of the impact of identified gene variants on aberrant splicing. We previously reported that single nucleotide variants (SNVs) in the last nucleotide of exons in COL4A5 cause aberrant splicing. It is known that the nucleotides located 2nd and 3rd to the last nucleotides of exons can also play an essential role in the first step of the splicing process. In this study, we aimed to investigate whether SNVs positioned 2nd or 3rd to the last nucleotide of exons in COL4A5 resulted in aberrant splicing.MethodsWe selected eight candidate variants: six from the Human Gene Variant Database Professional and two from our cohort. We performed an in-vitro splicing assay and reverse transcription-polymerase chain reaction (RT-PCR) for messenger RNA obtained from patients, if available.ResultsThe candidate variants were initially classified into the following groups: three nonsense, two missense, and three synonymous variants. Splicing assays and RT-PCR for messenger RNA revealed that six of the eight variants caused aberrant splicing. Four variants, initially classified as non-truncating variants, were found to be truncating ones, which usually show relatively more severe phenotypes.ConclusionWe revealed that exonic SNVs positioned 2nd or 3rd to the last nucleotide of exons in the COL4A5 were responsible for aberrant splicing. The results of our study suggest that attention should be paid when interpreting the pathogenicity of exonic SNVs near the 5′ splice site.

The novel HLA-B*15:638 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-B*15:638 differs from HLA-B*15:01:01:01 by one nucleotide in exon 2.

The novel HLA-DPB1*1352:01 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-DPB1*1352:01 differs from HLA-DPB1*02:01:02:01 by one nucleotide in exon 4.

The novel HLA-C*03:04:74 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-C*03:04:74 differs from HLA-C*03:04:01:01 by one nucleotide in exon 6.

The novel HLA-B*35:563 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-B*35:563 differs from HLA-B*35:03:01:01 by one nucleotide in exon 4.

The novel HLA-DRB1*14:246 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-DRB1*14:246 differs from HLA-DRB1*14:18 by one nucleotide in exon 2.

The novel HLA-B*52:110N allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-B*52:110N differs from HLA-B*52:01:01:01 by one nucleotide in exon 3.

The novel HLA-B*55:130 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-B*55:130 differs from HLA-B*55:35 by two nucleotides in exon 2.

The novel HLA-B*35:501 allele, identified by sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-B*35:501 differs from HLA-B*35:02:01:01 by three nucleotides in exon 2.

The novel HLA-C*06:02:102 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-C*06:02:102 differs from HLA-C*06:02:01:01 by one nucleotide in exon 2.

The novel HLA-C*03:04:99 allele, identified by sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-C*03:04:99 differs from HLA-C*03:04:01:01 by one nucleotide in exon 5.

Lipoid proteinosis: Novel ECM1 pathogenic variants and intrafamilial variability in four unrelated Arab families.

Lipoid proteinosis (LP) is a rare autosomal recessive multisystem disorder that is caused by loss-of-function pathogenic variants in the extracellular matrix protein-1 (ECM1) gene. The typical clinical manifestations of LP include hoarseness of voice, beaded papules on the eyelids, infiltration and scarring of the skin and mucosa, as well as neuropsychological abnormalities. Currently, more than 70 pathogenic variants have been reported, including nonsense, missense, splice site, deletion and insertion pathogenic variants, and more than half of them occurred in exons 6 and 7. Clinical evaluation and Sanger sequencing were performed on eight patients from four unrelated Arab families. We identified two novel ECM1 variants, one nonsense pathogenic variant in exon 6 (c.579G>A, p.Trp193*) and a deletion of three nucleotides (c.1390_1392del, p.Glu464del) in exon 9, and two previously reported frameshift variants; c.692_693delAG, in exon 6 and c.11dupC in exon 1. Although all patients had characteristic manifestations of lipoid proteinosis, we observed intrafamilial phenotypic variability. Our data expand the pathogenic variant spectrum of ECM1 and also supports the fact that exon 6 is one of the most common hot spots of pathological variants in ECM1.

A Unique Mechanism of a Novel Synonymous PHEX Variant Causing X-Linked Hypophosphatemia.

Synonymous mutations are usually nonpathogenic. We report here a family with X-linked hypophosphatemia (XLH) due to a novel synonymous PHEX variant with a unique mechanism. We studied a 4-member family (a mother, a son, and 2 daughters), all affected with XLH. Genomic DNA was extracted from peripheral leucocytes. Whole exome sequencing (WES) was used to identify the underlying genetic variant in the proband (the son). Sanger sequencing was used to confirm this variant in the proband and his family members. RT-PCR and sequencing of the cDNA revealed the effect of this variant on the PHEX structure and function. A synonymous variant in the PHEX gene (c.1701A>C) was identified in all affected members. This variant changes the first nucleotide of exon 17 from adenine to cytosine. Using RT-PCR, this variant was shown to interfere with splicing of exons 16 with 17 resulting in a single shorter PHEX transcript in the proband compared to normal control. Sanger sequencing of the cDNA revealed a complete skipping of exon 17 and direct splicing of exons 16 and 18. This led to a frameshift and an introduction of a new stop codon in the next codon (codon 568), which ultimately led to truncation and loss of the final 183 amino acids of PHEX. This novel variant shows how a synonymous exonic mutation may induce a complex series of changes in the transcription and translation of the gene and causes a disease, a mechanism that is not commonly recognized.

A novel HLA allele, HLA-A*03:420, identified by next-generation sequencing.

HLA-A*03:420 differs from HLA-A*03:01:01:01 by a single nucleotide in exon 1, codon -22.

Thrombosis in patients with hereditary fibrinogen deficiency

Introduction. In most cases, in patients with hereditary fibrinogen deficiency, clinical manifestations are represented by bleeding of varying intensity and localization. However, the clinical picture of hereditary fibrinogen deficiency can also be represented by thrombosis.Aim — to characterize the detected mutations in fibrinogen genes and to analyze prothrombotic factors in patients with hereditary hypofibrinogenemia and thrombosis.Materials and methods. Forty-nine patients with hereditary hypofibrinogenemia were observed, of which 46 patients had no history of thrombosis and 3 patients had a confirmed history of thrombosis. These 3 patients made up the study group.Results. Heterozygous mutations were found in all 3 patients in the fibrinogen gamma chain gene (FGG), one of them had a previously undescribed deletion g.2653_2684+211del, p.(Asp167Glufs*2), which removes 32 terminal nucleotides of the fifth exon of the FGG gene and leads to the formation of a stop codon in place of amino acid 168. In two other patients, there were missense mutations c.1140T>A, p.(Cys365Ser) and c.1114A>T, p.(Asp356Val), which can determine the thrombogenic properties of the altered protein structure of fibrinogen. Other prothrombotic factors were also identified: genetic polymorphisms of low thrombotic risk, surgery, taking combined oral contraceptives.Conclusion. Hereditary fibrinogen deficiency does not play a protective role in relation to the development of thrombosis and may cause the development of thrombosis, which is associated with its multifunctional role in the hemostasis system. The pathogenesis of thrombosis in patients with hereditary hypofibrinogenemia is multifactorial and may be associated with the characteristics of the main protein defect and the coexistence of hereditary and acquired thrombotic risk factors (surgical interventions, taking combined oral contraceptives, etc.).

Characterization of the NGP4A Gene in Regulating Grain Number Per Panicle of Rice (Oryza sativa L.)

Grain number per panicle (GNPP) is a major factor influencing rice yield (Oryza sativa L.). However, the molecular mechanisms of GNPP determination are not well understood. A rice GNPP mutant, ngp4a, was isolated from an ethyl methanesulfonate-mutagenized rice library of japonica Nipponbare. ngp4a produced fewer grains than wild-type plants at maturity as the number of secondary branches decreased significantly. The mutant phenotype of ngp4a was controlled by a recessive nuclear gene, which was fine-mapped into a 155.2 kb region on chromosome 4. One GNPP-related gene, Gnp4/LAX2 (LOC_Os04g32510), was found in the mapped region. The deletion of 3-bp nucleotides in the first exon of NGP4A resulted in a threonine residue loss. The mutation in NGP4A was responsible for the mutant phenotype of ngp4a. These results suggest that NGP4A is a new allele for Gnp4 and LAX2, while the mutant phenotype and underlying causation differed. Notably, transcriptome analysis revealed that NGP4A could regulate GNPP determination through the phenylpropanoid biosynthesis and mitogen-activated protein kinase signaling pathways. Our results further elucidated the vital roles of Gnp4/LAX2 in GNPP determination, providing a new genetic resource and theoretical basis to further explore the molecular mechanisms of GNPP in rice.

Detection of the HLA-B*15:01:74 allele, an HLA-B*15 variant discovered in a Japanese individual.

HLA-B*15:01:74 differs from B*15:01:01:01 by one nucleotide in exon 2 at position 470.