scholarly journals Genotyping of ABCC8, KCNJ11, and HADH in Iranian Infants with Congenital Hyperinsulinism

2021 ◽  
Vol 2021 ◽  
pp. 1-6
Author(s):  
Somayyeh Hashemian ◽  
Reza Jafarzadeh Esfehani ◽  
Siroos Karimdadi ◽  
Nosrat Ghaemi ◽  
Peyman Eshraghi ◽  
...  
Keyword(s):  
Mutational Analysis ◽  
Genetic Diagnosis ◽  
Case Series ◽  
Missense Variant ◽  
Congenital Hyperinsulinism ◽  
Biochemical Tests ◽  
Functional Studies ◽  
Pathogenic Variants ◽  
Abcc8 Gene ◽  
Kcnj11 Gene

Background. Congenital hyperinsulinism (CHI) is a heterogeneous disease with various underlying genetic causes. Among different genes considered effective in the development of CHI, ABCC8, KCNJ11, and HADH genes are among the important genes, especially in a population with a considerable rate of consanguineous marriage. Mutational analysis of these genes guides clinicians to better treatment and prediction of prognosis for this rare disease. The present study aimed to evaluate genetic variants in ABCC8, KCNJ11, and HADH genes as causative genes for CHI in the Iranian population. Methods. The present case series took place in Mashhad, Iran, within 11 years. Every child who had a clinical phenotype and confirmatory biochemical tests of CHI enrolled in this study. Variants in ABCC8, KCNJ11, and HADH genes were analyzed by the polymerase chain reaction and sequencing in our patients. Results. Among 20 pediatric patients, 16 of them had variants in ABCC8, KCNJ11, and HADH genes. The mean age of genetic diagnosis was 18.6 days. A homozygous missense (c.2041-21G > A) mutation in the ABCC8 gene was seen in three infants. Other common variants were frameshift variants (c.3438dup) in the ABCC8 gene and a missense variant (c.287-288delinsTG) in the KCNJ11 gene. Most of the variants in our population were still categorized as variants of unknown significance and only 7 pathogenic variants were present. Conclusion. Most variants were located in the ABCC8 gene in our population. Because most of the variants in our population are not previously reported, performing further functional studies is warranted.

scholarly journals A novel nonsense variant of the AGXT identified in a Chinese family: special variant research in the Chinese reference genome

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chang Bao Xu ◽  
Xu Dong Zhou ◽  
Hong En Xu ◽  
Yong Li Zhao ◽  
Xing Hua Zhao ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Reference Genome ◽  
Genetic Diagnosis ◽  
Primary Hyperoxaluria ◽  
Missense Variant ◽  
Population Heterogeneity ◽  
Chinese Family ◽  
Pathogenic Variants ◽  
Variation Database ◽  
Genetic Level

Abstract Background Primary hyperoxaluria(PH)is a rare autosomal recessive genetic disease that contains three subtypes (PH1, PH2 and PH3). Approximately 80% of PH patients has been reported as subtype PH1, this subtype of PH has been related to a higher risk of renal failure at any age. Several genetic studies indicate that the variants in gene AGXT are responsible for the occurrence of PH1. However, the population heterogeneity of the variants in AGXT makes the genetic diagnosis of PH1 more challenging as it is hard to locate each specific variant. It is valuable to have a complete spectrum of AGXT variants from different population for early diagnosis and clinical treatments of PH1. Case presentation In this study, We performed high-throughput sequencing and genetic analysis of a 6-year-old male PH1 patient from a Chinese family. Two variants (c.346G > A: p.Gly116Arg; c.864G > A: p.Trp288X) of the gene AGXT were identified. We found a nonsense variant (c.864G > A: p.Trp288X) that comes from the proband’s mother and has never been reported previously. The other missense variant (c.346G > A: p.Gly116Arg) was inherited from his father and has been found previously in a domain of aminotransferase, which plays an important role in the function of AGT protein. Furthermore, we searched 110 pathogenic variants of AGXT that have been reported worldwide in healthy local Chinese population, none of these pathogenic variants was detected in the local genomes. Conclusions Our research provides an important diagnosis basis for PH1 on the genetic level by updating the genotype of PH1 and also develops a better understanding of the variants in AGXT by broadening the variation database of AGXT according to the Chinese reference genome.

scholarly journals A novel TSC2 c.4511 T > C missense variant associated with tuberous sclerosis complex

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Shunzhi He ◽  
Na Lv ◽  
Hongchu Bao ◽  
Xiong Wang ◽  
Jing Li
Keyword(s):  
Tuberous Sclerosis ◽  
Tuberous Sclerosis Complex ◽  
Genetic Diagnosis ◽  
Missense Variant ◽  
Sporadic Case ◽  
Hereditary Disease ◽  
Multiple Organ ◽  
Cardiac Rhabdomyoma ◽  
Pathogenic Variants ◽  
Organ Systems

Abstract Background Tuberous sclerosis complex (TSC) is an autosomal-dominant hereditary disease characterized by hamartomas of multiple organ systems, including the brain, skin, heart, kidney and lung. Genetically, TSC is caused by pathogenic variants in the TSC1 or TSC2 gene. Case presentation We reported a sporadic case of a 32-year-old Han Chinese male diagnosed with TSC, whose spouse had a history of two spontaneous miscarriages and an induced abortion of a 30-week fetus identified with cardiac rhabdomyoma by ultrasound. A novel heterozygous missense variant in the TSC2 gene (Exon35:c.4511 T > C:p.L1504P) was identified in the male patient and the aborted fetus by next-generation sequencing, but not in his wife or both his parents. According to the ACMG/AMP criteria, this variant was classified as a “likely pathogenic” variant. Conclusion The novel TSC2:c.4511 T > C variant identified was highly likely associated with TSC and could potentially lead to adverse reproductive outcomes. IVF-ET and pre-implantation genetic diagnosis for TSC are recommended for this patient in the future to prevent fetal TSC.

scholarly journals Clinical and genetic characterization of congenital hyperinsulinism in Spain

2016 ◽  
Vol 174 (6) ◽  
pp. 717-726 ◽  
Author(s):  
R Martínez ◽  
C Fernández-Ramos ◽  
A Vela ◽  
T Velayos ◽  
A Aguayo ◽  
...  
Keyword(s):  
Mutational Analysis ◽  
Genetic Diagnosis ◽  
Clinical Information ◽  
Severe Hypoglycemia ◽  
Compound Heterozygous ◽  
Congenital Hyperinsulinism ◽  
Glucose Levels ◽  
Blood Glucose Levels ◽  
Lower Blood ◽  
Design And Methods

Context Congenital hyperinsulinism (CHI) is a clinically and genetically heterogeneous disease characterized by severe hypoglycemia caused by inappropriate insulin secretion by pancreatic β-cells. Objective To characterize clinically and genetically CHI patients in Spain. Design and methods We included 50 patients with CHI from Spain. Clinical information was provided by the referring clinicians. Mutational analysis was carried out for KCNJ11, ABCC8, and GCK genes. The GLUD1, HNF4A, HNF1A, UCP2, and HADH genes were sequenced depending on the clinical phenotype. Results We identified the genetic etiology in 28 of the 50 CHI patients tested: 21 had a mutation in KATP channel genes (42%), three in GLUD1 (6%), and four in GCK (8%). Most mutations were found in ABCC8 (20/50). Half of these patients (10/20) were homozygous or compound heterozygous, with nine being unresponsive to diazoxide treatment. The other half had heterozygous mutations in ABCC8, six of them being unresponsive to diazoxide treatment and four being responsive to diazoxide treatment. We identified 22 different mutations in the KATP channel genes, of which ten were novel. Notably, patients with ABCC8 mutations were diagnosed earlier, with lower blood glucose levels and required higher doses of diazoxide than those without a genetic diagnosis. Conclusions Genetic analysis revealed mutations in 56% of the CHI patients. ABCC8 mutations are the most frequent cause of CHI in Spain. We found ten novel mutations in the KATP channel genes. The genetic diagnosis is more likely to be achieved in patients with onset within the first week of life and in those who fail to respond to diazoxide treatment.

Identification of a pathogenic CARD14 mutation in a 70-year-old woman with pityriasis rubra pilaris: when genetic diagnosis influences choice of treatment strategy

2021 ◽  
Vol 14 (1) ◽  
pp. e235287
Author(s):  
Rikke Maria Nielsen ◽  
Stine Bjørn Gram ◽  
Anette Bygum
Keyword(s):  
Genetic Diagnosis ◽  
Missense Variant ◽  
Palmoplantar Keratoderma ◽  
Domain Family ◽  
Remarkable Effect ◽  
Familial Cases ◽  
Pityriasis Rubra Pilaris ◽  
Pathogenic Variants ◽  
Choice Of Treatment

Pityriasis rubra pilaris (PRP) is a rare dermatosis characterised by hyperkeratotic follicular papules, orange-red scaly plaques and palmoplantar keratoderma. The aetiology of the disease is in most cases unclear and treatment can be challenging. Familial cases of PRP may result from pathogenic variants in the caspase recruitment domain family member 14 (CARD14). We present a case of lifelong PRP in a 70-year-old woman, where genetic testing revealed a heterozygote missense variant c.412G>A, p.(Glu138Lys) in CARD14. Therapy with ustekinumab was initiated with remarkable effect, which improved the patient’s quality of life significantly.

scholarly journals Expanding the Phenotype of TUBB2A-Related Tubulinopathy: Three Cases of a Novel, Heterozygous TUBB2A Pathogenic Variant p.Gly98Arg

2020 ◽  
pp. 1-8
Author(s):  
Lindsey Schmidt ◽  
Karen E. Wain ◽  
Catherine Hajek ◽  
Juvianee I. Estrada-Veras ◽  
Maria J. Guillen Sacoto ◽  
...  
Keyword(s):  
Developmental Delay ◽  
Case Series ◽  
Missense Variant ◽  
Autism Spectrum ◽  
Cortical Dysplasia ◽  
Global Developmental Delay ◽  
Tubulin Genes ◽  
Pathogenic Variants ◽  
Brain Malformations ◽  
History Of

Tubulinopathies are a group of conditions caused by variants in 6 tubulin genes that present with a spectrum of brain malformations. One of these conditions is <i>TUBB2A</i>-related tubulinopathy. Currently, there are 9 reported individuals with pathogenic variants within the <i>TUBB2A</i> gene, with common manifestations including, but not limited to, global developmental delay, seizures, cortical dysplasia, and dysmorphic corpus callosum. We report 3 patients identified by exome and genome sequencing to have a novel, pathogenic, missense variant in <i>TUBB2A</i> (p.Gly98Arg). They presented similarly with intellectual disability, hypotonia, and global developmental delay and varied with respect to the type of cortical brain malformation, seizure history, diagnosis of autism spectrum disorder, and other features. This case series expands the natural history of <i>TUBB2A</i>-related tubulinopathy while describing the presentation of a novel, pathogenic, missense variant in 3 patients.

scholarly journals Aberrant Splicing in the PKD2 Gene as a Cause of Polycystic Kidney Disease

1999 ◽  
Vol 10 (11) ◽  
pp. 2342-2351 ◽  
Author(s):  
DAVID M. REYNOLDS ◽  
TOMOHITO HAYASHI ◽  
YIQIANG CAI ◽  
BARBERA VELDHUISEN ◽  
TERRY J. WATNICK ◽  
...  
Keyword(s):  
Kidney Disease ◽  
Polycystic Kidney Disease ◽  
Splice Variants ◽  
Missense Variant ◽  
Single Base Substitution ◽  
Base Substitution ◽  
Polycystic Kidney ◽  
Single Base ◽  
Functional Studies ◽  
Pathogenic Variants

Abstract. It is estimated that approximately 15% of families with autosomal dominant polycystic kidney disease (ADPKD) have mutations in PKD2. Identification of these mutations is central to identifying functionally important regions of gene and to understanding the mechanisms underlying the pathogenesis of the disorder. The current study describes mutations in six type 2 ADPKD families. Two single base substitution mutations discovered in the ORF in exon 14 constitute the most COOH-terminal pathogenic variants described to date. One of these mutations is a nonsense change and the other encodes an apparent missense variant. Reverse transcription-PCR from patient lymphoblast RNA showed that, in addition, both mutations resulted in out-of-frame splice variants by activating cryptic splice sites via different mechanisms. The apparent missense variant produced such a strong splicing signal that the processed transcript from the mutant chromosome did not contain any of the normally spliced, missense product. A third mutation, a nonconservative missense change effecting a negatively charged residue in the third transmembrane span, is likely pathogenic and defines a highly conserved residue consistent with a potential channel subunit function for polycystin-2. The remaining three mutations included two frame shifts resulting from deletion of one or two bases in exons 6 and 10, respectively, and a nonsense mutation due to a single base substitution in exon 4. The study also defined a novel intragenic polymorphism in exon 1 that will be useful in analyzing “second hits” in PKD2. Finally, the study demonstrates that there are reduced levels of normal polycystin-2 protein in lymphoblast lines from PKD2-affected individuals and that truncated mutant polycystin-2 cannot be detected in patient lymphoblasts, suggesting that the latter may be unstable in at least some tissues. The mutations described will serve as critical reagents for future functional studies in PKD2.

scholarly journals Clinical and Genetic Characterization of 153 Patients with Persistent or Transient Congenital Hyperinsulinism

2020 ◽  
Vol 105 (4) ◽  
pp. e1686-e1694
Author(s):  
Jonna M E Männistö ◽  
Maleeha Maria ◽  
Joose Raivo ◽  
Teemu Kuulasmaa ◽  
Timo Otonkoski ◽  
...  
Keyword(s):  
Glucose Metabolism ◽  
Katp Channel ◽  
Genetic Diagnosis ◽  
Cross Sectional Study ◽  
Congenital Hyperinsulinism ◽  
Inadequate Response ◽  
Phenotypic Data ◽  
Cross Sectional ◽  
Targeted Next Generation Sequencing ◽  
Pathogenic Variants

Abstract Context Major advances have been made in the genetics and classification of congenital hyperinsulinism (CHI). Objective To examine the genetics and clinical characteristics of patients with persistent and transient CHI. Design A cross-sectional study with the register data and targeted sequencing of 104 genes affecting glucose metabolism. Patients Genetic and phenotypic data were collected from 153 patients with persistent (n = 95) and transient (n = 58) CHI diagnosed between 1972 and 2015. Of these, 86 patients with persistent and 58 with transient CHI participated in the analysis of the selected 104 genes affecting glucose metabolism, including 10 CHI-associated genes, and 9 patients with persistent CHI were included because of their previously confirmed genetic diagnosis. Main outcome measures Targeted next-generation sequencing results and genotype–phenotype associations. Results Five novel and 21 previously reported pathogenic or likely pathogenic variants in ABCC8, KCNJ11, GLUD1, GCK, HNF4A, and SLC16A1 genes were found in 68% (n = 65) and 0% of the patients with persistent and transient CHI, respectively. KATP channel mutations explained 82% of the mutation positive cases. Conclusions The genetic variants found in this nationwide CHI cohort are in agreement with previous studies, mutations in the KATP channel genes being the major causes of the disease. Pathogenic CHI-associated variants were not identified in patients who were both diazoxide responsive and able to discontinue medication within the first 4 months. Therefore, our results support the notion that genetic testing should be focused on patients with inadequate response or prolonged need for medication.

scholarly journals Characterization of ABCC8 and KCNJ11 gene mutations and phenotypes in Korean patients with congenital hyperinsulinism

2011 ◽  
Vol 164 (6) ◽  
pp. 919-926 ◽  
Author(s):  
So Eun Park ◽  
Sarah E Flanagan ◽  
Khalid Hussain ◽  
Sian Ellard ◽  
Choong Ho Shin ◽  
...  
Keyword(s):  
Mutational Analysis ◽  
Gene Mutations ◽  
Heterozygous Mutation ◽  
Congenital Hyperinsulinism ◽  
Sulfonylurea Receptor ◽  
Korean Patients ◽  
Kcnj11 Gene ◽  
Common Causes ◽  
Channel Mutation ◽  
Inherited Mutations

ObjectiveCongenital hyperinsulinism (CHI) is characterized by persistent hypoglycemia due to the inappropriate insulin secretion. Inactivating mutations in the ABCC8 and KCNJ11 genes, which encode the sulfonylurea receptor 1 and Kir6.2 subunits of the ATP-sensitive K+ (KATP) channel in pancreatic β-cell, are the most common cause of CHI. We studied the genetic etiology and phenotypes of CHI in Korean patients.MethodsABCC8 and KCNJ11 mutational analysis was performed in 17 patients with CHI. Medical records were retrospectively reviewed to identify phenotypes.ResultsMutations (12 ABCC8 and three KCNJ11) were identified in 82% (14/17) of patients. Of these, nine ABCC8 mutations (E100X, W430X, c.1630+1G>C, D813N, Q923X, E1087_A1094delinsDKSDT, Q1134H, H1135W, and E1209Rfs) and one KCNJ11 mutation (W91X) were novel. Of the 14 patients, four had confirming recessively inherited CHI. The remaining ten patients had single heterozygous mutations. The majority (12/17) of patients were medically responsive. Of the five diazoxide-responsive patients, four had an ABCC8 mutation. The five patients unresponsive to medical management and one diazoxide-responsive patient underwent pancreatectomy and had diffuse histology. Of the operated six patients, two had recessively inherited mutations; three patients had a single heterozygous mutation (one maternally and two paternally inherited); and one patient had no identifiable KATP channel mutation.ConclusionsThis is the first study to report genotype and phenotype correlations among Korean patients with CHI. Mutations in ABCC8 and KCNJ11 are the most common causes of CHI in Korean patients. Similar to other studies, there is marked genetic heterogeneity and no clear genotype–phenotype correlation.

scholarly journals Human Missense Variation is Constrained by Domain Structure and Highlights Functional and Pathogenic Residues

2017 ◽  
Author(s):  
Stuart A. MacGowan ◽  
Fábio Madeira ◽  
Thiago Britto-Borges ◽  
Melanie S. Schmittner ◽  
Christian Cole ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Prediction Models ◽  
Domain Architecture ◽  
Ring Finger ◽  
Missense Variant ◽  
Protein Domain ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Functional Studies ◽  
Pathogenic Variants

Human genome sequencing has generated population variant datasets containing millions of variants from hundreds of thousands of individuals1-3. The datasets show the genomic distribution of genetic variation to be influenced on genic and sub-genic scales by gene essentiality,1,4,5 protein domain architecture6 and the presence of genomic features such as splice donor/acceptor sites.2 However, the variant data are still too sparse to provide a comparative picture of genetic variation between individual protein residues in the proteome.1,6 Here, we overcome this sparsity for ∼25,000 human protein domains in 1,291 domain families by aggregating variants over equivalent positions (columns) in multiple sequence alignments of sequence-similar (paralagous) domains7,8. We then compare the resulting variation profiles from the human population to residue conservation across all species9 and find that the same tertiary structural and functional pressures that affect amino acid conservation during domain evolution constrain missense variant distributions. Thus, depletion of missense variants at a position implies that it is structurally or functionally important. We find such positions are enriched in known disease-associated variants (OR = 2.83, p ≈ 0) while positions that are both missense depleted and evolutionary conserved are further enriched in disease-associated variants (OR = 1.85, p = 3.3×10-17) compared to those that are only evolutionary conserved (OR = 1.29, p = 4.5×10-19). Unexpectedly, a subset of evolutionary Unconserved positions are Missense Depleted in human (UMD positions) and these are also enriched in pathogenic variants (OR = 1.74, p = 0.02). UMD positions are further differentiated from other unconserved residues in that they are enriched in ligand, DNA and protein binding interactions (OR = 1.59, p = 0.003), which suggests this stratification can identify functionally important positions. A different class of positions that are Conserved and Missense Enriched (CME) show an enrichment of ClinVar risk factor variants (OR = 2.27, p = 0.004). We illustrate these principles with the G-Protein Coupled Receptor (GPCR) family, Nuclear Receptor Ligand Binding Domain family and In Between Ring-Finger (IBR) domains and list a total of 343 UMD positions in 211 domain families. This study will have broad applications to: (a) providing focus for functional studies of specific proteins by mutagenesis; (b) refining pathogenicity prediction models; (c) highlighting which residue interactions to target when refining the specificity of small-molecule drugs.

scholarly journals Identification of a Novel Variant of ARHGAP29 in a Chinese Family with Nonsyndromic Cleft Lip and Palate

2020 ◽  
Vol 2020 ◽  
pp. 1-6
Author(s):  
Jian-Xia Tang ◽  
Xiang-Shui Xiao ◽  
Kai Wang ◽  
Jie-Yuan Jin ◽  
Liang-Liang Fan ◽  
...  
Keyword(s):  
Cleft Lip ◽  
Cleft Lip And Palate ◽  
Genetic Diagnosis ◽  
Missense Variant ◽  
Bioinformatic Analysis ◽  
Chinese Family ◽  
Pathogenic Variants ◽  
Whole Exome ◽  
Novel Variant ◽  
Development Methods

Background. Cleft lip with or without cleft palate (CL/P) is the most common facial birth defect, with a worldwide incidence of 1 in 700-1000 live births. CL/P can be divided into syndromic CL/P (SCL/P) and nonsyndromic CL/P (NSCL/P). Genetic factors are an important component to the etiology of NSCL/P. ARHGAP29, one of the NSCL/P disease-causing genes, mediates the cyclical regulation of small GTP binding proteins such as RhoA and plays an essential role in cellular shape, proliferation, and craniofacial development. Methods. The present study investigated a Chinese family with NSCL/P and explored potential pathogenic variants using whole-exome sequencing (WES). Variants were screened and filtered through bioinformatic analysis and prediction of variant pathogenicity. Cosegregation was subsequently conducted. Results. We identified a novel heterozygous missense variant of ARHGAP29 (c.2615C > T, p.A872V) in a Chinese pedigree with NSCL/P. Conclusion. We detected the disease-causing variant in this NSCL/P family. Our identification expands the genetic spectrum of ARHGAP29 and contributes to novel approaches to the genetic diagnosis and counseling of CL/P families.

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