Novel truncating germline variant reinforces TINF2 as a susceptibility gene for familial non-medullary thyroid cancer.

BACKGROUND: It has long been observed that there are families in which non-medullary thyroid cancer (NMTC) occurs, but few syndromes and genes have been described to date. Proteins in the shelterin complex have been implied in cancer. Here, we have studied shelterin genes in families affected by NMTC (FNMTC). METHODS: We performed whole-exome sequencing (WES) in 10 affected individuals from four families with at least three affected members. Polymerase chain reaction (PCR) and Sanger sequencing were performed to search for variants in the TINF2 gene in 40 FNMTC families. TINF2 transcripts and loss of heterozygosity (LOH) were studied in several affected patients of one family. RESULTS: We found the c.507G>T variant in heterozygosis in the TINF2 gene in one family, co-segregating in all five affected members. This variant affects the normal splicing. LOH was not observed. CONCLUSIONS: Our results reinforce the TINF2 gene as a susceptibility cause of FNMTC suggesting the importance of location of frameshift variants in TINF2. According to our data and previous literature, TINF2 pathogenic variants appear to be a significant risk factor for the development of NMTC and/or melanoma.

A novel single-base deletional mutation of MIP impairs protein distribution and cell-to-cell adhesion in autosomal dominant cataracts in a Chinese family.

Congenital cataracts are the leading cause of irreversible visual disability in children, and genetic factors play an important role in their development. In this study, targeted exome sequencing revealed a novel single-base deletional mutation of MIP (c.301delG; p.Ala101Profs*16) segregated with congenital punctate cataract in a Chinese family. The hydrophobic properties, and secondary and tertiary structures for truncated MIP were predicted to affect the function of protein by bioinformatics analysis. When MIP-WT and MIP-Ala101fs expression constructs were singly transfected into HeLa cells, it was found that the mRNA level showed no significant difference, while the protein level of the mutant was remarkably reduced compared to that of the wild-type MIP. Immunofluorescence images showed that the MIP-WT was principally localized to the plasma membrane, whereas the MIP-Ala101fs protein was aberrantly trapped in the cytoplasm. Furthermore, the cell-to-cell adhesion capability and the cell-to-cell communication property were both significantly reduced for MIP-Ala101fs compared to the MIP-WT (all *p < 0.05). This is the first report of the c.301delG mutation in the MIP gene associated with autosomal dominant congenital cataracts. We propose that the cataract is caused by the decreased protein expression and reduced cell-to-cell adhesion by the mutant MIP. The impaired trafficking or instability of the mutant protein, as well as compromised intercellular communication is probably a concurrent result of the mutation. The results expand the genetic and phenotypic spectra of MIP and help to better understand the molecular basis of congenital cataracts.

SERPINC1 c.1247dupC: a novel SERPINC1 gene mutation associated with familial thrombosis results in a secretion defect and quantitative antithrombin deficiency.

BACKGROUND: Antithrombin (AT) is an important anticoagulant in hemostasis. We describe here the characterization of a novel AT mutation associated with clinically relevant thrombosis. A pair of sisters with confirmed type I AT protein deficiency was genetically analyzed on suspicion of an inherited SERPINC1 mutation. A frameshift mutation, c.1247dupC, was identified and the effect of this mutation was examined on the cellular and molecular level. METHODS: Plasmids for the expression of wild-type (WT) and mutated SERPINC1 coding sequence (CDS) fused to green fluorescent protein (GFP) or hemagglutinin (HA) tag were transfected into HEK293T cells. Subcellular localization and secretion of the respective fusion proteins were analyzed by confocal laser scanning microscopy and Western blot. RESULTS: The c.1247dupC mutation results in a frameshift in the CDS of the SERPINC1 gene and a subsequently altered amino acid sequence (p.Ser417LysfsTer48). This alteration affects the C-terminus of the AT antigen and results in impaired secretion as confirmed by GFP- and HA-tagged mutant AT analyzed in HEK293T cells. CONCLUSION: The p.Ser417LysfsTer48 mutation leads to impaired secretion, thus resulting in a quantitative AT deficiency. This is in line with the type I AT deficiency observed in the patients.

Newborn Screening for ß-Thalassemia Identifies a Complex Genotype Involving a Novel ß-Globin Gene Mutation (HBB:c.336dup).

Newborn screening identified a Chinese-Canadian infant who was positive for possible ß-thalassemia (ß-thal). Detailed family studies demonstrated that the proband was a compound heterozygote for the Chinese Gγ(Aγδß)0-thal deletion and a novel frameshift mutation within exon 3 (HBB:c.336dup), and heterozygous for the Southeast Asian α-thal deletion (--SEA/αα). This case illustrates the importance of follow-up molecular testing of positive newborn screening results to confirm the diagnosis and define risks for future pregnancies.

A Novel Frameshift Mutation(HBA2:C.337delC) Associated With α-Thalassemia Trait Detected by Next-Generation Sequencing in Southern China.

Here, we report a novel frameshift mutation caused by a single base deletion in exon 3 of the HBA2 gene (HBA2:c.337delC) detected by next-generation sequencing. The proband was a 26-year-old Chinese pregnant woman who originates from Hunan Province. Her mean corpuscular volume(MCV) and mean corpuscular hemoglobin (MCH) had a mild decrease. Capillary electrophoresis (CE) showed that both Hb A (97.8%) and Hb F (0.0%) values were within normal range, while the Hb A2 (2.2%) value was below normal. Sequence analysis of the α and ß-globin genes revealed a novel single base deletion at codon 112 (HBA2:c.337delC) in the heterozygous state, which resulted in a mild phenotype of α-thalassemia.

A Novel Frameshift Mutation of HBB Causing Dominant ß-Thalassemia in a Chinese Individual.

We reported a rare ß-thalassemia patient, a 41-year-old Chinese male with small cell hypopigmentation anemia, jaundice and splenomegaly as the main clinical symptoms. By using Next-Generation Sequencing (NGS), we identified a novel de novo HBB mutation(c.358_365dup, p.Phe123Alafs*39) which resulted in an abnormally prolonged ß-globin chain comprising 159 amino acid residues. The secondary and three-dimensional structures of the ß-globin predicted that the novel prolonged ß-globin chain has a considerable risk of instability in the hemoglobin, and leads to clinical phenotype. This study contributes to the enrichment of the genetic pathogenic mutation database for thalassemia and underscores the significance of NGS in the screening of mutations for thalassemia families.

CRISPR/Cas9 Vector Construction for Gene Knockout.

This protocol outlines the construction of a plant transformation plasmid to express both the Cas9 nuclease and individual guide RNA (gRNA), facilitating the induction of double-stranded breaks (DSBs) in DNA and subsequent imprecise repair via the non-homologous end-joining (NHEJ) pathway. The gRNA expression cassettes are assembled from three components. First, the Medicago truncatula U6.6 (MtU6) promoter (352 bp) and scaffold (83 bp) sequences are amplified from a pUC-based plasmid. Additionally, a third fragment, corresponding to the target sequence, is synthesized as an oligonucleotide. The three gRNA expression fragments are then loosely assembled in a ligation-free cloning reaction and used as a template for an additional PCR step to amplify a single gRNA expression construct, ready for assembly into the transformation vector. The benefits of this design include cost efficiency, as subsequent cloning reactions only require 59 oligonucleotides and standard cloning reagents. Researchers engaged in CRISPR/Cas9-mediated genome editing in plants will find this protocol a clear and resource-efficient approach to create transformation plasmids for their experiments.

Case report: A novel PTCH1 frameshift mutation leading to nevoid basal cell carcinoma syndrome.

A patient presenting with several basal cell carcinomas, pigmented nevi, and developmental defects was diagnosed with nevoid basal cell carcinoma syndrome. Gene panel sequencing and Sanger sequencing were used to identify a novel heterozygous frameshift mutation, c.1312dupA:p.Ser438Lysfs, in exon 9 of PTCH1. I-Tasser and PyMol analyses indicated that the mutated protein patched homolog 1 (PTCH1) lacked 12 transmembrane domains and the intracellular and extracellular rings of ECD2 compared with the wild-type protein, resulting in a remarkably different structure from that of the wild-type protein. This case extends our knowledge of the mutation spectrum of NBCCS.

Identification and functional analysis of first heterozygous frameshift mutation in the GHRH gene in a Chinese boy with isolated growth hormone deficiency.

BACKGROUND: Isolated growth hormone deficiency (IGHD) is a rare genetically heterogeneous disorder caused primarily by mutations in GH1 and GH releasing hormone receptor (GHRHR). The aim of this study was to identify the molecular etiology of a Chinese boy with IGHD. METHODS: Whole-exome sequencing, sanger sequencing and bioinformatic analysis were performed to screen for candidate mutations. The impacts of candidate mutation on gene expression, intracellular localization and protein function were further evaluated by in vitro assays. RESULTS: A novel heterozygous frameshift mutation in the GHRH gene (c.91dupC, p.R31Pfs*98) was identified in a Chinese boy clinically diagnosed as having IGHD. The mutation was absent in multiple public databases, and considered as deleterious using in silico prediction, conservative analysis and three-dimensional homology modeling. Furthermore, mRNA and protein expression levels of mutant GHRH were significantly increased than wild-type GHRH (p < 0.05). Moreover, mutant GHRH showed an aberrant accumulation within the cytoplasm, and obviously reduced ability to stimulate GH secretion and cAMP accumulation in human GHRHR-expressing pituitary GH3 cells compared to wild-type GHRH (p < 0.05). CONCLUSION: Our study discovered the first loss-of function mutation of GHRH in a Chinese boy with IGHD and provided new insights on IGHD pathogenesis caused by GHRH haploinsufficiency.

A Hemoglobinopathy That Produces an Array of Different Hemoglobin A1c Values.

Hemoglobin A1c (HbA1c) refers to non-enzymatically glycated hemoglobin and reflects the patient's glycemic status over approximately 3 months. An elevated HbA1c over 6.5% National Glycohemoglobin Standardization Program (NGSP) (48 mmol/mol the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC)) can be used to diagnose diabetes mellitus. In our laboratory, HbA1c is determined by ion-exchange chromatography which has the advantage of detecting common Hb variants such as Hb S, C, E and D without adversely affecting the HbA1c determination. Certain homozygous or compound heterozygous hemoglobinopathies such as homozygous sickle disease and Hb SC disease can significantly lower the HbA1c by reducing red cell lifespan. Occasionally however, rare and mostly benign hemoglobinopathies can interfere with this technique resulting in an apparent elevation of HbA1c in an otherwise non-diabetic patient. In this report, we describe such a hemoglobinopathy termed Hb Wayne that resulted in a significant HbA1c elevation in a normoglycemic individual. HbA1c was determined by multiple methods including immunoassay, a modified capillary electrophoresis and an alternative ion-exchange system. These techniques yielded significantly lower A1c results, more in keeping with the patient's clinical background. The alternative ion-exchange system resulted in a low A1c that was qualified by warning flags on the chromatogram that indicated the result was not reportable. The hemoglobinopathy in question, Hb Wayne, is a frameshift mutation in the alpha globin gene that results in an extended alpha globin polypeptide that can form two variants Hb Wayne I and Wayne II. Hb Wayne is a clinically silent asymptomatic disorder with no hematologic consequences. The artifactual elevation of HbA1c is, in contrast, very significant because it may result in a misdiagnosis of diabetes mellitus leading to unnecessary treatment. In this report, we compare our findings with other descriptions of Hb Wayne in the literature and corroborate a number of previous observations and conclusions.

A family with nine siblings showing signs of Rothmund-Thomson syndrome with two being definitely diagnosed with the syndrome due to homozygous N-terminal mutation of RECQL4.

This study presents a family with nine children, two of them diagnosed with RTS2 using genetic testing. The other siblings show some of the RTS2 criteria and are suggestive of the syndrome. Such reports help physicians be more alert in dealing with cases of rare syndromes. Timely initiation of genetic counseling and testing once the first child was diagnosed with the syndrome could have prevented the birth of affected siblings by RTS2. Since RTS2 patients could have a severe clinical manifestation as osteosarcoma which probably leads to death at a young age, the importance of genetic testing is even more underlined.

In silico prediction, molecular modeling, and dynamics studies on the targeted next-generation sequencing identified genes underlying congenital heart disease in Down syndrome patients.

Background: Individuals with Down syndrome (DS) have a 40%-60% chance of being born with congenital heart disease (CHD). This indicates that CHD in individuals with DS is not solely caused by trisomy 21, and there may be other genetic factors contributing to the development of CHD in these children. A study has identified variants in the specific genes that contribute to the pathogenesis of CHD in children with DS, isolated DS, and the CHD group. Computational studies on these identified variants, which, together with trisomy 21, determine the risk for CHD in DS cases, were limited. Here, we aimed to identify the impact of the identified variants that contribute to the pathogenesis of CHD in children with DS through in silico prediction, molecular modeling, and dynamics studies. Methodology and Results: The target single-nucleotide polymorphisms included in the study were examined for pathogenicity, residue conservation, and protein structural changes. The structural predictions were done using I-TASSER, Robetta, SWISS-MODEL, and Phyre2 tools. Further, the predicted models were validated through the PROCHECK server and molecular dynamics simulation using GROMACS software. The conservation analysis conducted on the identified variant highlights its significance in relation to the genetic disorders. Furthermore, a dynamics simulation study revealed the impact of the variant on protein structural stability (≤3 Å), providing valuable insights into its pathogenicity. We have also observed that the structure of the centrosomal protein of 290 kDa gene is relatively unstable, which may be attributed to its exclusive inclusion of helices within its secondary structural components. Conclusions: This computational study explores, for the first time, the association between genes and CHD-DS, evaluating the identified specific frameshift variants. The observed pathogenic mutations in CHD-DS patients require further experimental validation and may contribute to the development of prospective drug design research. The insights gained from the structural and functional implications of these variants could potentially serve as a cornerstone in the development of effective treatments for this debilitating condition.

Identification of novel variants in retinitis pigmentosa genes by whole-exome sequencing

SUMMARY OBJECTIVE: Retinitis pigmentosa is an inherited degenerative disorder causing severe retinal dystrophy and visual impairment, mainly with onset in the first or second decades. The next-generation sequencing has become an efficient tool to identify disease-causing mutations in retinitis pigmentosa. The aim of this retrospective study was to investigate novel gene variants and evaluate the utility of whole-exome sequencing in patients with retinitis pigmentosa. METHODS: The medical records of 20 patients with retinitis pigmentosa at Eskişehir City Hospital between September 2019 and February 2022 were analyzed retrospectively. Peripheral venous blood was obtained, followed by the extraction of genomic DNAs. The medical and ophthalmic histories were collected, and ophthalmological examinations were performed. Whole-exome sequencing was performed to determine the genetic etiology of the patients. RESULTS: The proportion of genetically solved cases was 75% (15/20) in the patients with retinitis pigmentosa. Molecular genetic testing identified 13 biallelic and 4 monoallelic mutations in known retinitis pigmentosa genes, including 11 novel variants. According to in silico prediction tools, nine variants were predicted as pathogenic or possibly pathogenic. We identified six previously reported mutations to be associated with retinitis pigmentosa. The age of onset of the patients ranged from 3 to 19, with a mean age of onset of 11.6. All patients had a loss of central vision. CONCLUSION: As the first study of the application of whole-exome sequencing among patients with retinitis pigmentosa in a Turkish cohort, our results may contribute to the characterization of the spectrum of variants related to retinitis pigmentosa in the Turkish population. Future population-based studies will enable us to reveal the detailed genetic epidemiology of retinitis pigmentosa.

Whole-exome sequencing identified a homozygous novel RAG1 mutation in a child with omenn syndrome

Introduction and objectives Omenn syndrome (OS) is a very rare type of severe combined immunodeficiencies manifested with erythroderma, eosinophilia, hepatosplenomegaly, lymph-adenopathy, and elevated level of serum IgE. OS is inherited with an autosomal recessive mode of inheritance. Germline mutations in the human RAG1 gene cause OS. Materials and methods In this study, we investigated a 2-month-old boy with cough, mild anaemia, pneumonia, immunodeficiency, repeated infection, feeding difficulties, hepatomegaly, growth retardation, and heart failure. Parents of the proband were phenotypically normal. Results Karyotype analysis and chromosomal microarray analysis found no chromosomal structural abnormalities (46, XY) and no pathogenic copy number variations (CNVs) in the proband. Whole-exome sequencing identified a novel homozygous single nucleotide deletion (c.2662delC) in exon 2 of the RAG1 gene in the proband. Sanger sequencing confirmed that both the proband parents were carrying this variant in a heterozygous state. This variant was not identified in two elder sisters and one elder brother of the proband and in the 100 ethnically matched normal healthy individuals. This novel homozygous deletion (c.2662delC) leads to the frameshift, which finally results in the formation of the truncated protein (p.Leu888Phefs*3) V(D)J recombination-activating protein 1 with 890 amino acids compared with the wildtype V(D)J recombination-activating protein 1 of 1043 amino acids. Hence, it is a loss-of-function variant. Conclusion Our present study expands the mutational spectrum of the RAG1 gene associated with OS. We also strongly suggested the importance of whole-exome sequencing for the genetic screening of patients with OS (AU)

Wiedemann-Steiner syndrome with a novel pathogenic variant in KMT2A: a case report / Síndrome de Wiedemann-Steiner por una nueva variante patogénica en KMT2A: reporte de un caso

Abstract Case Description: We report the case of a one-year-old girl who was diagnosed with Wiedemann-Steiner Syndrome based on the identification of a novel de novo frameshift mutation in the KMT2A gene by whole exome sequencing and supported by her clinical features. Clinical Findings: KMT2A mutations cause Wiedemann-Steiner Syndrome, a very rare genetic disorder characterized by congenital hypertrichosis, short stature, intellectual disability, and distinct facial features. Treatment and Outcome: Whole exome sequencing identified a novel frameshift variant: c. 4177dupA (p.Ile1393Asnfs * 14) in KMT2A; this change generates an alteration of the specific binding to non-methylated CpG motifs of the DNA to the protein. The genotype and phenotype of the patient were compared with those of earlier reported patients in the literature. Clinical Relevance: In diseases with low frequency, it is necessary to establish a genotype-phenotype correlation that allows the establishment of therapeutic and follow-up goals. The phenotype comparation with other reported cases did not show differences attributable to sex or age among patients with Wiedemann-Steiner Syndrome. Whole exome sequencing allows identifying causality in conditions with high clinical and genetic heterogeneity like hypertrichosis.

Resumen Descripción del caso: Se reporta el caso de una paciente femenina de un año de edad, diagnosticada con Síndrome de Wiedemann-Steiner basado en la identificación de una nueva variante patogénica de novo de tipo frameshift en el gen KMT2A Mediante secuenciación de exoma usando el enfoque de trio, sumado a sus características clínicas. Hallazgos clínicos: las mutaciones en KMT2A causan el Síndrome de Wiedemann-Steiner, un desorden genético muy raro caracterizado por hipertricosis congénita, talla baja, retardo mental variable y fenotipo facial distintivo, los cuales se encuentran en la paciente reportada. Resultado: La Secuenciación de exoma completo encontró una variante de tipo frameshift: c.4177dupA (p. Ile1393Asnfs * 14) en KMT2A, este cambio a nivel génico genera una alteración de la unión específica a motivos CpG no metilados del DNA a la proteína. El genotipo y el fenotipo de la paciente fue comparado con los pacientes reportados previamente en la literatura. Relevancia clínica: En enfermedades con baja frecuencia como la aquí reportada es necesario establecer correlaciones genotipo-fenotipo que permitan establecer planes terapéuticos y de seguimiento. El análisis realizado no evidenció diferencias atribuibles a sexo o edad entre los pacientes diagnosticados con Síndrome de Weidemann-Steiner. La secuenciación de exoma permitió identificar causalidad en este caso, cuya característica principal de hipertricosis se asocia con alta heterogeneidad clínica y genética.

Birt-Hogg-Dubé syndrome / Sindrome de Birt-Hogg-Dube

A 45-year-old woman with a history of renal carcinoma was observed for facial, cervical and truncal flesh-colored papules. Relatives had similar skin findings and a brother had repeated episodes of pneumothorax. The computerized tomography scan revealed multiple cysts on both lungs. A skin biopsy revealed a perifollicular fibroma. The clinical diagnosis of Birt-Hogg-Dubé syndrome (BHDS) was corroborated by identification of a novel frameshift c.573delGAinsT (p.G191fsX31) mutation in heterozygosity on exon 6 of the folliculin gene. The presence of multiple and typical benign hair follicle tumors highlights the role of the dermatologist in the diagnosis of this rare genodermatosis that is associated with an increased risk of renal cell cancer and pulmonary cysts, warranting personal and familial follow-up and counseling.

Uma mulher de 45 anos com história de carcinoma renal foi observada por pápulas cor da pele, faciais, cervicais e tronculares. Referia história familiar de achados cutâneos semelhantes e irmão com episódios repetidos de pneumotórax. Identificaram-se múltiplos quistos pulmonares por tomografia computorizada. Uma biópsia cutânea revelou fibroma perifolicular. O diagnóstico clínico de síndrome de Birt-Hogg-Dubé (BHDS) foi contudo corroborado pela identificação de uma nova mutação frameshift c.573delGAinsT (p.G191fsX31) em heterozigotia no exão 6 do gene da foliculina. A presença de múltiplos e típicos tumores benignos do folículo piloso, realça o papel do dermatologista no diagnóstico desta rara genodermatose, que está associada a um risco aumentado de tumores de células renais e cistos pulmonares, exigindo seguimento e aconselhamento pessoal e familiar.

Identification of a novel mutation in DAX1/NR0B1A gene in two siblings with severe clinical presentation of adrenal hypoplasia congenita / Identificação de nova mutação no gene DAX1/NR0B1A em dois irmãos com forma clínica grave de hipoplasia adrenal congênita

OBJECTIVE: To search for mutations in DAX1/NR0B1A gene in siblings to establish the molecular etiology of the adrenal hypoplasia congenita (AHC), a rare potentially life-threatening disorder. CASE REPORT: We describe two siblings who presented with salt-wasting syndrome in the newborn period and received hormonal replacement for primary adrenal insufficiency. A diagnostic hypothesis of AHC was suspected because the children maintained, during hormonal treatment, low plasma 17-OH progesterone (17-OHP) and androgens, despite high ACTH levels. RESULTS: DAX1 gene was studied by molecular analysis, which showed a mutation, confirming the diagnosis in the siblings and a heterozygous state in the mother. Direct sequencing of DAX1 revealed an insertion of an adenine base (c1382-1383 A ins), which lead to a pMet461Asp substitution. CONCLUSION: A novel frameshift mutation of DAX1 gene, which established the molecular etiology of the AHC in the siblings, was identified. Obtaining a precise genetic diagnosis of this adrenal disorder, which, sometimes, cannot be confirmed only by clinical aspects, may have important implications for the long-term management of the disease.

OBJETIVO: Pesquisar mutações no gene DAX1/NR0B1A em dois irmãos com suspeita de hipoplasia adrenal congênita (HAC), rara doença potencialmente fatal, para estabelecer sua etiologia molecular. RELATO DOS CASOS: São apresentados os relatos de dois irmãos com síndrome perdedora de sal no período neonatal que receberam terapia de reposição hormonal para insuficiência adrenal primária. O diagnóstico de HAC foi suspeitado porque as crianças mantiveram, durante o tratamento hormonal, níveis plasmáticos reduzidos de 17-OH-progesterona e andrógenos ao lado de níveis elevados de ACTH. RESULTADOS: A análise molecular do gene DAX1 mostrou a mutação, confirmando o diagnóstico nos irmãos e o estado heterozigoto da mãe. No sequenciamento direto do DAX1 foi encontrada inserção de uma adenina (c1382-1383 A ins), levando à substituição pMet461Asp. CONCLUSÃO: Uma nova mutação da fase de leitura no gene DAX1 foi identificada, estabelecendo a etiologia molecular da HAC nos dois irmãos. Um diagnóstico genético preciso deste distúrbio adrenal, frequentemente não confirmado apenas pelos aspectos clínicos, pode ter importantes implicações para o manuseio em longo prazo da doença.