Variability of clinical and biochemical phenotype in liver phosphorylase kinase deficiency with variants in the phosphorylase kinase (PHKG2) gene

2020 ◽  
Vol 33 (9) ◽  
pp. 1117-1123
Author(s):  
Nadia Waheed ◽  
Anjum Saeed ◽  
Sadaqat Ijaz ◽  
Zafar Fayyaz ◽  
Muhammad Nadeem Anjum ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Laboratory Data ◽  
In Silico Analysis ◽  
Missense Variant ◽  
Phosphorylase Kinase ◽  
Type I ◽  
Rare Type ◽  
Elevated Liver Enzymes ◽  
Novel Variants ◽  
Glycogenosis Type

AbstractBackgroundPHKG2-related liver phosphorylase kinase deficiency is inherited in autosomal recessive pattern and is a rare type of liver glycogenosis. We demonstrated the clinical presentation and genetic determinants involved in children with PHKG2- related liver phosphorylase kinase deficiency.MethodologyTen Pakistani children with liver phosphorylase kinase from seven different families, were enrolled over a period of 18 months. All regions of the PHKG2 gene spanning exons and splicing sites were evaluated through targeted exome sequencing. Variants were analyzed using different bioinformatics tools. Novel variants were reconfirmed by direct sequencing.ResultsSeven different variants were identified in PHKG2 gene including five novel variants: three stop codons (c.226C>T [p.R76*], c.454C>T [p.R152*] and c.958C>T [p.R320*]), one missense variant c.107C>T (p.S36F) and one splice site variant (c.557-3C>G). All five novel variants were predicted to be damaging by in Silico analysis. The variants are being transmitted through recessive pattern of inheritance except one family (two siblings) has compound heterozygotes. Laboratory data revealed elevated transaminases and triglycerides, normal creatinine phosphokinase and uric acid levels but with glycogen loaded hepatocytes on liver histology.ConclusionPHKG2 related liver phosphorylase kinase deficiency can mimic both liver glycogenosis type I (glucose-6-phosphatase deficiency) & III(amylo-1,6 glucosidase) and characterized by early childhood onset of hepatomegaly, growth restriction, elevated liver enzymes and triglycerides. Molecular analysis would be helpful in accurate diagnosis and proper treatment. The symptoms and biochemical abnormalities in liver glycogenosis due phosphorylase kinase deficiency tend to improve with proper dietary restrictions but need to be monitored for long-term complications such as liver fibrosis and cirrhosis.

scholarly journals Mutation Spectrum and Genotype–Phenotype Analyses in a Pakistani Cohort With Hemophilia B

2017 ◽  
Vol 24 (5) ◽  
pp. 741-748 ◽  
Author(s):  
Muhammad Tariq Masood Khan ◽  
Arshi Naz ◽  
Jawad Ahmed ◽  
Tahir Shamsi ◽  
Shariq Ahmed ◽  
...  
Keyword(s):  
Clinical Phenotype ◽  
Direct Sequencing ◽  
In Silico Analysis ◽  
Genetic Alterations ◽  
Factor Ix ◽  
Hemophilia B ◽  
Mutation Spectrum ◽  
Coagulation Activity ◽  
Exon 2 ◽  
Novel Variants

This study aimed to (1) identify F9 genetic alterations in patients with hemophilia B (HB) of Pakistani origin and (2) determine the genotype–phenotype relationships in these patients. Diagnosed cases of HB were identified through registries at designated tertiary health-care centers across the country. Consenting patients were enrolled into the study. The factor IX (FIX) coagulation activity (FIX:C) and key clinical features were recorded. Direct sequencing of F9 was carried out in all patients. All the variants identified were analyzed for functional consequences employing in silico analysis tools. Accession numbers from National Center of Biotechnology Information ClinVar database were retrieved for the novel variants. Genotype–FIX:C relationships were determined followed by FIX:C clinical phenotype assessment. A total of 52 patients with HB from 36 unrelated families were identified, which mainly comprised patients with moderate HB (n = 35; 67.3%). Among these, 35 patients from 22 unrelated families could be contacted and enrolled into the study. Missense variants were the most frequent (58.8%), followed by nonsense variants (17.6%). A missense, a short insertion, and a nonsense novel variants in exon 2, 6, and 7, respectively, were also identified. The disease manifested FIX:C heterogeneity in relation to the corresponding mutation in a significant number of cases. Clinical phenotype heterogeneity was also observed in relation to FIX:C-based severity assessment. We concluded that the registered FIX-deficient population of Pakistan mainly comprises moderate HB. F9 mutation spectrum in Pakistani patients with HB is heterogeneous. The HB population of Pakistan manifests a significant amount of genotype–FIX:C and FIX:C–clinical phenotype heterogeneities.

Homozygous Novel Variants in the Glycine Decarboxylase Gene Associated with Nonketotic Hyperglycinemia in a Distinct Population

2021 ◽  
Author(s):  
Heba Salah Abdelkhalek Elabd ◽  
Fatma Bastaki ◽  
Mohamed Khalifa
Keyword(s):  
Middle Eastern ◽  
In Silico Analysis ◽  
Autosomal Recessive Disorder ◽  
Missense Variant ◽  
Primary Defect ◽  
Pathogenic Variants ◽  
Glycine Encephalopathy ◽  
Novel Variants ◽  
Glycine Cleavage ◽  
Nonketotic Hyperglycinemia

AbstractGlycine encephalopathy (GE), also known as nonketotic hyperglycinemia (NKH) is an autosomal recessive disorder due to a primary defect in the glycine cleavage enzyme system. It is characterized by elevated levels of glycine in the plasma and cerebrospinal fluid (CSF) and increased CSF to plasma glycine ratio.Mutations in three genes of the mitochondrial glycine cleavage system have been found to cause NKH. Most patients have a mutation in the GLDC.In this report, we present five new patients from Middle Eastern families with NKH. They were all born to consanguineous parents and two of them have family history of similarly affected sibling(s). All patients presented with neonatal encephalopathy associated with seizures. Their diagnoses were suspected clinically and confirmed biochemically.DNA sequence analysis of the five patients revealed five different pathogenic or likely pathogenic variants in the GLDC. Three were missense variants (c.2675C > T; p.Ala892Val), (c.2512A > G; p.Asn838Asp), and (c.2943A > C; p.Lys981Asn); one was an intronic missense variant (c.1402–2A > T) leading to an exonic deletion, and one was a deletion of 42 amino acids (c.1927-?_2052 + ?del.) All variants were novel and homozygous. The pathogenicity of these variants was determined according to the American College of Medical Genetics (ACMG) variant classification and in silico analysis. Another novel homozygous variant (c.1384C > G; p.Leu462Val) was detected, which was classified as likely benign.The novel variants identified in the GLDC in these patients underlie the pathogenesis of NKH, specifically for the Middle Eastern population. This expands the mutation spectrum of NKH to include a distinct ethnic population that has not been studied before.

scholarly journals Incomplete Segregation of MSH6 Frameshift Variants with Phenotype of Lynch Syndrome

2017 ◽  
Author(s):  
Raffaella Liccardo ◽  
Marina De Rosa ◽  
Giovanni Battista Rossi ◽  
Nicola Carlomagno ◽  
Paola Izzo ◽  
...  
Keyword(s):  
Lynch Syndrome ◽  
In Silico ◽  
Stop Codon ◽  
Direct Sequencing ◽  
Premature Stop Codon ◽  
In Silico Analysis ◽  
Frameshift Deletion ◽  
The Family ◽  
Novel Variants ◽  
Repair Genes

Background: Lynch syndrome, the most frequent form of hereditary colorectal cancer and involves mutations in mismatch repair genes. The aim of this study was to identify mutations in MSH6 from 97 subjects negative for mutations in MLH1 and MSH2. Methods: By direct sequencing, we identified 27 MSH6 variants, of which, nine were novel. To verify the pathogenicity of these novel variants we performed in silico and segregation analyses. Results: Three novel variants were predicted by in silico analysis as damaging mutations and segregated with the disease phenotype. While, a novel frameshift deletion variant that was predicted to yield a premature stop codon, did not segregate with the LS phenotype in 3 of 4 cases in the family. Interestingly, another frame-shift variant identified in this study, already described in the literature, also did not segregate with the LS phenotype in 1 of 2 affected subjects in the family. In all affected subjects of both families, no mutation was detected in other MMR genes. Therefore, it is expected that within these families other genetic factors contribute to the disease either alone or in combination with MSH6 variants. Conclusion: We conclude that caution should be exercised in counseling for MSH6-associated LS family members.

Molecular Analysis of the CYP11B2 Gene in 62 Patients with Hypoaldosteronism Due to Aldosterone Synthase Deficiency

2020 ◽  
Vol 106 (1) ◽  
pp. e182-e191
Author(s):  
Christina Merakou ◽  
Irene Fylaktou ◽  
Amalia Sertedaki ◽  
Maria Dracopoulou ◽  
Antonis Voutetakis ◽  
...  
Keyword(s):  
Gene Sequencing ◽  
Failure To Thrive ◽  
In Silico Analysis ◽  
Autosomal Recessive Disorder ◽  
Molecular Study ◽  
Aldosterone Synthase ◽  
Salt Wasting ◽  
Pathogenic Variants ◽  
Novel Variants ◽  
Aldosterone Synthase Deficiency

Abstract Context Isolated congenital hypoaldosteronism presents in early infancy with symptoms including vomiting, severe dehydration, salt wasting, and failure to thrive. The main causes of this rare autosomal recessive disorder is pathogenic variants of the CYP11B2 gene leading to aldosterone synthase deficiency. Objective To investigate the presence of CYP11B2 pathogenic variants in a cohort of patients with a clinical, biochemical, and hormonal profile suggestive of aldosterone synthase deficiency. Design Clinical and molecular study. Setting Tertiary academic Children’s Hospital, Center for Rare Pediatric Endocrine Diseases. Patients and Methods Sixty-two patients (56 unrelated patients and 6 siblings), with hypoaldosteronism and their parents, underwent CYP11B2 gene sequencing after its selective amplification against the highly homologous CYP11B1 gene. In silico analysis of the identified novel variants was carried out to evaluate protein stability and potential pathogenicity. Results CYP11B2 gene sequencing revealed that 62 patients carried a total of 12 different pathogenic CYP11B2 gene variants, 6 of which are novel. Importantly, 96% of the 56 patients carried the previously reported p.T185I variant either in homozygosity or in compound heterozygosity with another variant. The 6 novel variants detected were: p.M1I, p.V129M, p.R141Q, p.A165T, p.R448C, and the donor splice site variant of intron 8, c.1398 + 1G > A. Conclusion Molecular diagnosis was achieved in 62 patients with aldosterone synthase deficiency, the largest cohort thus far reported. Six novel genetic variants were identified as possibly pathogenic, extending the spectrum of reported molecular defects of the CYP11B2 gene.

The Molecular Basis of Antithrombin Deficiency in Belgian and Dutch Families

1998 ◽  
Vol 80 (09) ◽  
pp. 376-381 ◽  
Author(s):  
W. Lissens ◽  
S. Seneca ◽  
P. Capel ◽  
B. Chatelain ◽  
P. Meeus ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Gene Deletion ◽  
Direct Sequencing ◽  
Genetic Defect ◽  
Polymorphism Analysis ◽  
Type I ◽  
Type Ii ◽  
Antithrombin Deficiency ◽  
Venous Thromboembolic Events ◽  
At Deficiency

SummaryThe molecular basis of hereditary antithrombin (AT) deficiency has been investigated in ten Belgian and three Dutch unrelated kindreds. Eleven of these families had a quantitative or type I AT deficiency, with a history of major venous thromboembolic events in different affected members. In the other two families a qualitative or type II AT deficiency was occasionally diagnosed.DNA studies of the AT gene were performed, using polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) analysis, followed by direct sequencing of the seven exons and intronexon junction regions. Six novel point mutations were identified: four missense, one nonsense mutation and a single nucleotide deletion near the reactive site, causing a frameshift with premature translation termination. In two kindreds the underlying genetic defect was caused by a whole gene deletion, known as a rare cause of AT deficiency. In these cases, Southern blot and polymorphism analysis of different parts of the AT gene proved useful for diagnosis. In another kindred a partial gene deletion spanning 698 basepairs could precisely be determined to a part of intron 3B and exon 4. In two type I and in both type II AT deficient families a previously reported mutation was identified. In all cases, the affected individuals were heterozygous for the genetic defect.

Glycogenosis type I – von Gierke disease

2020 ◽  
pp. 439-448
Author(s):  
William L. Nyhan ◽  
Georg F. Hoffmann ◽  
Aida I. Al-Aqeel ◽  
Bruce A. Barshop
Keyword(s):  
Type I ◽  
Glycogenosis Type

scholarly journals Clinical and Genetic Characteristics of COL2A1-Associated Skeletal Dysplasias in 60 Russian Patients: Part I

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 137
Author(s):  
Tatyana Markova ◽  
Vladimir Kenis ◽  
Evgeniy Melchenko ◽  
Darya Osipova ◽  
Tatyana Nagornova ◽  
...  
Keyword(s):  
Clinical Manifestations ◽  
Normal Growth ◽  
Type I ◽  
Syndrome Type ◽  
Stickler Syndrome ◽  
Genetic Characteristics ◽  
Col2a1 Gene ◽  
Skeletal Dysplasias ◽  
Spondyloepiphyseal Dysplasia ◽  
Novel Variants

The significant variability in the clinical manifestations of COL2A1-associated skeletal dysplasias makes it necessary to conduct a clinical and genetic analysis of individual nosological variants, which will contribute to improving our understanding of the pathogenetic mechanisms and prognosis. We presented the clinical and genetic characteristics of 60 Russian pediatric patients with type II collagenopathies caused by previously described and newly identified variants in the COL2A1 gene. Diagnosis confirmation was carried out by new generation sequencing of the target panel with subsequent validation of the identified variants using automated Sanger sequencing. It has been shown that clinical forms of spondyloepiphyseal dysplasias predominate in childhood, both with more severe clinical manifestations (58%) and with unusual phenotypes of mild forms with normal growth (25%). However, Stickler syndrome, type I was less common (17%). In the COL2A1 gene, 28 novel variants were identified, and a total of 63% of the variants were found in the triple helix region resulted in glycine substitution in Gly-XY repeats, which were identified in patients with clinical manifestations of congenital spondyloepiphyseal dysplasia with varying severity, and were not found in Stickler syndrome, type I and Kniest dysplasia. In the C-propeptide region, five novel variants leading to the development of unusual phenotypes of spondyloepiphyseal dysplasia have been identified.

scholarly journals A Case Report of Apert Syndrome in a Fifty-Eight Year Old Female

2020 ◽  
Vol 3 (11) ◽  
pp. 352-354
Author(s):  
Pooja Gaur
Keyword(s):  
Case Report ◽  
Clinical Care ◽  
Open Bite ◽  
Apert Syndrome ◽  
Facial Features ◽  
Type I ◽  
Anterior Open Bite ◽  
Rare Type ◽  
Patient Reported ◽  
Hands And Feet

Defined as a rare type I acrocephalosyndactyly syndrome which is clinically characterized by dysmorphic facial features, craniosynostosis, and severe syndactyly of the hands and feet, Apert Syndrome represents an autosomal dominant inheritance which occurs due to the gene mutations in the receptors of the fibroblast growth factor. Oral lesions include tooth crowding, reduction in the size of the maxilla, impacted teeth, anterior open-bite, ectopic eruption, delayed eruption, thick gingiva and supernumerary teeth. The present case report describes a 58 year old female patient reported with the features of Apert’s syndrome such as dysmorphic facial features, occular anomalies, syndactyly and oral features. The case was referred to a specialized centre of clinical care for further treatment.

scholarly journals Central Precocious Puberty in a Girl and Early Puberty in Her Brother Caused by a Novel Mutation in the MKRN3 Gene

2014 ◽  
Vol 99 (4) ◽  
pp. E647-E651 ◽  
Author(s):  
Nikolaos Settas ◽  
Catherine Dacou-Voutetakis ◽  
Maria Karantza ◽  
Christina Kanaka-Gantenbein ◽  
George P. Chrousos ◽  
...  
Keyword(s):  
Precocious Puberty ◽  
Novel Mutation ◽  
Structural Alignment ◽  
In Silico Analysis ◽  
Missense Variant ◽  
Central Precocious Puberty ◽  
Dimensional Structure ◽  
Sex Characteristics ◽  
Coding Region ◽  
Early Puberty

Context: Central precocious puberty (CPP), defined as the development of secondary sex characteristics prior to age 8 years in girls and 9 years in boys, results from the premature activation of the hypothalamic-pituitary-gonadal axis. Mutations in the imprinted gene MKRN3 have been recently implicated in familial cases of CPP. Objective: The objective of the study was to uncover the genetic cause of CPP in a family with two affected siblings. Design and participants: The entire coding region of the paternally expressed MKRN3 gene was sequenced in two siblings, a girl with CPP and her brother with early puberty, their parents, and their grandparents. Results: A novel heterozygous missense variant in the MKRN3 gene (p.C340G) was detected in the two affected siblings, their unaffected father, and the paternal grandmother. As expected, the mutated allele followed an imprinted mode of inheritance within the affected family. In silico analysis predicts the mutation as possibly damaging in all five software packages used. Furthermore, structural alignment of the ab initio native and mutant MKRN3 models predicts that the p.C340G mutation leads to significant structural perturbations in the 3-dimensional structure of the C3HC4 really interesting new gene motif of the protein, further emphasizing the functional implications of the novel MKRN3 alteration. Conclusions: We report a novel MKRN3 mutation (p.C340G) in a girl with CPP and her brother with early puberty. MKRN3 alterations should be suspected in all cases with familial CPP or early puberty, especially if male patients are also involved or the precocious puberty trend does not follow the usually observed mother-to-daughter inheritance.

The Clinical, Biochemical, and Familial Presentation of Type V Hyperlipoproteinemia in Childhood

PEDIATRICS ◽  
1977 ◽  
Vol 59 (4) ◽  
pp. 513-525
Author(s):  
Peter O. Kwiterovich ◽  
J. Ramsay Farah ◽  
W. Virgil Brown ◽  
Paul S. Bachorik ◽  
Stephen B. Baylin ◽  
...  
Keyword(s):  
Insulin Level ◽  
Recurrent Abdominal Pain ◽  
Enzymatic Activities ◽  
Type I ◽  
Rare Type ◽  
Type Iv ◽  
Type V Hyperlipoproteinemia ◽  
Therapeutic Diets ◽  
Primary Type ◽  
Type V

Primary type V hyperlipoproteinemia was identified in two preadolescent children. The propositus (kindred N) was a 10-year-old girl with severely creamy plasma, lipemia retinalis, hypertriglyceridemia (triglyceride level, 6,800 mg/100 ml), and hypercholesterolemia (cholesterol level, 490 mg/100 ml). Her parents and an 8-year-old sister all had endogenous hypertriglyceridemia (type IV hyperlipoproteinemia). In kindred A, an 11-year-old boy had triglyceride levels as high as 1,100 mg/100 ml and recurrent abdominal pain. His father had type V hyperlipoproteinemia; his mother was normal. All three of his older teenage siblings had type IV hyperlipoproteinemia. The enzymatic activities of lipoprotein lipase (LPL), hepatic triglyceride lipase (HTL), and histaminase (H) were studied in postheparin plasma. The LPL level was low in the children and both parents in kindred N. LPL level in kindred A was normal, except for one child with type IV hyperlipoproteinemia. HTL level was normal to above normal in both kindreds. Most patients had a normal H level, but one parent (kindred N) had no preheparin H and very low levels of postheparin H. There was a strong correlation (r = 0.58, significant at < 1% level) between the release of LPL and H but not between HTL and H (r = 0.22). The mean (± 1 S.D.) levels of the enzymes were as follows: LPL, 2.8 ± 0.7 µmol/ml/hr in kindred N and 5.4 ± 2.2 µmol/ml/hr in kindred A; H, 13.4 ± 6.8 units/ml in kindred N and 22.0 ± 11.9 units/ml in kindred A; and HTL, 18.0 ± 7.1 µmol/ml/hr in kindred N and 14.9 ± 6.3 µmol/ml/hr in kindred A. The enzymatic activities of kindreds N and A were significantly different for LPL (P < .001) and H (.025 < P < .05) but not for HTL. All but one child had at least one high insulin level, which was accompanied by hyperglycemia in two children. The hypertriglyceridemia in all but one child was ameliorated on therapeutic diets. These data suggest that the genetic basis of the hypertriglyceridemia in these two families is different and that hyperchylomicronemia in childhood is not confined to the rare type I hyperlipoproteinemia.

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