Nonsense Pathogenic Variant Research Articles

Variability in proliferative and migratory defects in Hirschsprung disease-associated RET pathogenic variants.

Despite the extensive genetic heterogeneity of Hirschsprung disease (HSCR; congenital colonic aganglionosis) 72% of patients harbor pathogenic variants in 10 genes that form a gene regulatory network (GRN) controlling the development of the enteric nervous system (ENS). Among these genes, the receptor tyrosine kinase gene RET is the most significant contributor, accounting for pathogenic variants in 12%-50% of patients depending on phenotype. RET plays a critical role in the proliferation and migration of ENS precursors, and defects in these processes lead to HSCR. However, despite the gene's importance in HSCR, the functional consequences of RET pathogenic variants and their mechanism of disease remain poorly understood. To address this, we investigated the proliferative and migratory phenotypes in a RET-dependent neural crest-derived cell line harboring one of five missense (L56M, E178Q, Y791F, S922Y, F998L) or three nonsense (Y204X, R770X, Y981X) pathogenic heterozygous variants. Using a combination of cDNA-based and CRISPR-based PRIME editing coupled with quantitative proliferation and migration assays, we detected significant losses in cell proliferation and migration in three missense (E178Q, S922Y, F998L) and all nonsense variants. Our data suggests that the Y791F variant, whose pathogenicity has been debated, is likely not pathogenic. Importantly, the severity of migration loss did not consistently correlate with proliferation defects, and the phenotypic severity of nonsense variants was independent of their position within the RET protein. This study highlights the necessity and feasibility of targeted functional assays to accurately assess the pathogenicity of HSCR-associated variants, rather than relying solely on machine learning predictions, which could themselves be refined by incorporating such functional data.

A new nonsense pathogenic variant in exon 1 of PHOX2B leads to the diagnosis of congenital central hypoventilation syndrome with intra-familial variability

Congenital central hypoventilation syndrome (CCHS) is a rare genetic disorder of the autonomic nervous system resulting in decreased brain sensitivity to hypercapnia and hypoxia characterized by a genetic abnormality in the pair-like homeobox 2B (PHOX2B) gene. Most patients have a heterozygous expansion of the polyalanine repeat in exon 3 (PARM), while 10 % of patients have non-PARM (NPARM) mutations that can span the entire gene. The majority of pathogenic variants are de novo, but variants with incomplete penetrance can be identified in the heterozygous state. In the present report, CCHS was diagnosed in a symptomatic 3-month-old infant with neonatal respiratory distress. Genetic analysis revealed a new mutation in exon 1 of the PHOX2B gene – p.Ser28* (c.83C>G) – which was further identified in two family members, one minimally symptomatic and one asymptomatic. The identification of this new mutation supports the importance of sequencing the entire gene even when the classic PARM mutation is not found and highlights the phenotypic variability of CCHS.

A rare case report of the Cowden syndrome

Cowden syndrome (CS) is a rare autosomal dominant genodermatosis caused by a heterozygous germline mutation in the PTEN gene, found in nearly 80% of cases. It is characterized by multiple benign hamartomas which manifest across various organs. This condition is further distinguished by its association with macrocephaly, facial trichilemmomas, acral keratoses, papillomatous papules, and a heightened susceptibility to certain malignant neoplasms, particularly affecting the thyroid, endometrium, and the breast (OMIM no. 58350).In this report, we detail the case of an Indian patient presenting with macrocephaly and multiple blackish pigmented areas on the face, alongside several small papules on the dorsum of the hands, and the presence of gastric and duodenal polyps, among other symptoms. Genetic analysis through Sanger sequencing of the PTEN gene revealed a heterozygous nonsense pathogenic variant (ENST00000371953.8: c.388C > T, p.Arg130Ter), thereby confirming a CS diagnosis. The report encompasses a comprehensive review of the existing literature, emphasizing the significance of genetic evaluation and discussing the intricacies of managing patients diagnosed with CS.

Novel Pathogenic Variants Leading to Sporadic Amyotrophic Lateral Sclerosis in Greek Patients.

Amyotrophic lateral sclerosis (ALS) is a rapidly progressive disease that affects motor neurons, leading to paralysis and death usually 3-5 years after the onset of symptoms. The investigation of both sporadic and familial ALS highlighted four main genes that contribute to the pathogenesis of the disease: SOD1, FUS, TARDBP and C9orf72. This study aims to provide a comprehensive investigation of genetic variants found in SOD1, FUS and TARDBP genes in Greek sporadic ALS (sALS) cases. Our sequencing analysis of the coding regions of the abovementioned genes that include the majority of the variants that lead to ALS in 32 sALS patients and 3 healthy relatives revealed 6 variants in SOD1, 19 variants in FUS and 37 variants in TARDBP, of which the SOD1 p.D90A and the FUS c.*356G>A (rs886051940) variants have been previously associated with ALS, while two novel nonsense pathogenic variants were also identified, namely FUS p.R241* and TDP-43 p.Y214*. Our study contributes to the worldwide effort toward clarifying the genetic basis of sALS to better understand the disease's molecular pathology.

Prenatal diagnosis of dent disease type I with a nonsense pathogenic variant in CLCN5: a case study

IntroductionDent disease type I is a rare X-linked recessive renal tubular disease resulting from pathogenic variants in the CLCN5 gene. Due to the rarity of Dent disease type I and the diversity of its phenotypes, its clinical diagnosis is complex and poses a challenge to clinicians.MethodsA foetus and a child from a 36-year-old pregnant woman with a birth history of abnormal children were enrolled in this study. Pregnant women undergo amniocentesis for prenatal diagnosis at the gestational age of 12+ 3 weeks. Chromosomal microarray (CMA) analysis and whole-exome sequencing (WES) were employed to investigate the chromosomal copy number and single gene variants. Literature retrieval and data analysis were performed for genotype and phenotype collection analysis.ResultsNo chromosomal abnormalities or CNVs were detected in the entire family through karyotype and familial CMA analyses. WES identified a nonsense pathogenic variant in CLCN5 of the X chromosome, c.1942 C > T (exon 11, NM_000084), which was inherited from his mother, who exhibited regular clinical features.ConclusionThis study suggests that children with low-molecular-weight proteinuria and hypercalciuria should undergo prompt genetic testing to exclude Dent disease.

Severe Early-Onset Obesity and Diabetic Ketoacidosis due to a Novel Homozygous c.169C>T p.Arg57* Variant in CEP19 Gene

Introduction: Early-onset severe obesity is usually the result of an underlying genetic disorder, and several genes have recently been shown to cause syndromic and nonsyndromic forms of obesity. The “centrosomal protein 19 (CEP19)” gene encodes for a centrosomal and ciliary protein. Homozygous variants in the CEP19 gene are extremely rare causes of early-onset severe monogenic obesity. Herein, we present a Turkish family with early-onset severe obesity with variable features. Methods: Sanger sequencing and whole-exome sequencing were performed to identify the genetic etiology in the family. Results: The index case was a 12-year-old female who presented with severe obesity (BMI of 62.7 kg/m²), metabolic syndrome, and diabetic ketoacidosis. Her nonidentical twin female siblings also had early-onset severe obesity, metabolic syndrome, and diabetes. In addition, one of the affected siblings had situs inversus abdominalis, polysplenia, lumbar vertebral fusion, and abnormal lateralization. A novel homozygous nonsense (c.169C>T, p. Arg57*) pathogenic variant was detected in exon 3 of the CEP19 gene in all affected members of the family. One unaffected sister and unaffected parents were heterozygous for the variant. This variant is predicted to cause a stop codon at amino acid sequence 57, leading to a truncated CEP19 protein. Discussion/Conclusion: Our study expands the phenotypical manifestations and variation database of CEP19 variants. The findings in one of our patients reaffirm its role in the assembly and function of both motile and immotile cilia.

Higher Prevalence of Nonsense Pathogenic DMD Variants in a Single-Center Cohort from Brazil: A Genetic Profile Study That May Guide the Choice of Disease-Modifying Treatments.

Dystrophinopathies are muscle diseases caused by pathogenic variants in DMD, the largest gene described in humans, representing a spectrum of diseases ranging from asymptomatic creatine phosphokinase elevation to severe Duchenne muscular dystrophy (DMD). Several therapeutic strategies are currently in use or under development, each targeting different pathogenic variants. However, little is known about the genetic profiles of northeast Brazilian patients with dystrophinopathies. We describe the spectrum of pathogenic DMD variants in a single center in northeast Brazil. This is an observational, cross-sectional study carried out through molecular-genetic analysis of male patients diagnosed with dystrophinopathies using Multiplex Ligation-dependent Probe Amplification (MLPA) followed by Next-Generation Sequencing (NGS)-based strategies. A total of 94 male patients were evaluated. Deletions (43.6%) and duplications (10.6%) were the most recurring patterns of pathogenic variants. However, small variants were present in 47.1% of patients, most of them nonsense variants (27.6%). This is the largest South American single-center case series of dystrophinopathies to date. We found a higher frequency of treatment-amenable nonsense single-nucleotide variants than most previous studies. These findings may have implications for diagnostic strategies in less-known populations, as a higher frequency of nonsense variants may mean a higher possibility of treating patients with disease-modifying drugs.

FRI267 Carney Complex From A Single Familycarney Complex From A Single Family Followed Up Over 20 Years With Different Clinical Pattern Evolution

Abstract Disclosure: A.W. Kuhn: None. D.S. de Melo: None. H.L. Charchar: None. B.M. Mariani: None. M.Y. Nishi: None. F.L. Ledesma: None. F.Y. Tanno: None. V. Srougi: None. J.L. Chambo: None. A. Latronico: None. B.B. Mendonca: None. M.Q. Almeida: None. M.C. Fragoso: None. Background: Carney complex (CNC) is a hereditary syndrome with autosomal dominant inheritance, composed of multiple neoplasms, such as benign and malignant, endocrine and nonendocrine tumors (cardiac, cutaneous and neural). The primary pigmented nodular adrenocortical disease (PPNAD) is a rare cause of Cushing syndrome is the most common endocrine neoplasia in CNC. The most frequent genetic cause is related with the presence of germline pathogenic allelic variants on PRKAR1A. Overall CNC penetrance among carriers of the PRKAR1A allelic variant is approximately 97.5%, however, families with long-term follow up is rarely described in literature. Clinical Case: A 17-year-old male, was referred to our Hospital in 2003 due to weight gain (≈10 Kg), BMI 27.27 Kg/m2, acne, occurrence of abdomen purplish striae (>1cm), facial plethora and arrest of pubertal development for last 2 years. He has had pigmented facial lesions since 9 years old. Laboratory revealed suppressed ACTH <18.0 pg/mL, failure to suppress cortisol levels after low dose dexamethasone test (DST-1mg): cortisol 29 µg/dL (normal range: <1.8 µg/dL), and total urinary cortisol (TUC), 2809 µg/24 h (normal range: 30-300 µg/24h). Abdominal CT scan showed normal right adrenal gland and a micronodule (0.8 cm) in the left adrenal gland. Bone densitometry showed an important loss of density. Owing to ACTH-independent Cushing's syndrome and adrenal with micronodule, the most plausible diagnostic hypothesis was PPNAD associated to CNC. He underwent bilateral laparoscopic adrenalectomy and the histological data confirmed PPNAD on both adrenal glands. He developed primary adrenal insufficiency and he maintains continuous replacement with gluco and mineralocorticoids. The genetic analysis identified a heterozygous germline nonsense pathogenic variant on PRKAR1A (p.Tyr21X) in exon 2. His relatives, such as father, two younger sisters, one paternal aunt and a female cousin carried the same nonsense variant. All of them also presented facial lentiginous but without Cushing features. In the first investigation, all his relatives showed possible autonomous cortisol secretion. In follow-up of almost 20 years, the index case and his family members did not develop other manifestations of CNC. Only his father developed metabolic syndrome, but all relatives maintained subclinical hypercortisolism due to possible autonomous cortisol secretion without any clinical repercussions. Clinical Lessons: Carney complex is a rare disease and the follow-up of familial cases over the years can show different clinical pattern despite the same germline pathogenic variant. Probably somatic molecular mechanisms as modulators could trigger specifically clinical manifestations. Presentation: Friday, June 16, 2023

Novel pathogenic variants in SPARC as cause of osteogenesis imperfecta: Two case reports

Pathogenic variants in SPARC cause a rare autosomal recessive form of osteogenesis imperfecta (OI), classified as OI type XVII, which was first reported in 2015. Only six patient cases with this specific form of OI have been reported to date. The SPARC protein plays a crucial role in the calcification of collagen in bone, synthesis of the extracellular matrix, and the regulation of cell shape. In this case report, we describe the phenotype of two patients with SPARC-related OI, including a patient with two novel pathogenic variants in the SPARC gene. Targeted Next Generation Sequencing revealed new compound heterozygous variants (c.484G > A p.(Glu162Lys)) and c.496C > T p.(Arg166Cys)) in one patient and a homozygous nonsense pathogenic variant (c.145C > T p.(Gln49*)) in the other. In line with previously reported cases, the two OI patients presented delayed motor development, muscular weakness, scoliosis, and multiple fractures. Interestingly, our study reports for the first time the occurrence of dentinogenesis imperfecta. The study also reports the effectiveness of bisphosphonate treatment for OI type XVII. This article enhances the genetic, clinical, therapeutic, and radiological understanding of SPARC-related OI.

Clinical and molecular characterization of parathyroid carcinoma in multiple endocrine neoplasia type 1.

Nineteen cases of parathyroid carcinoma in patients with multiple endocrine neoplasia type 1 have been reported in the literature, of which 11 carry an inactivating germline mutation in the MEN1 gene. Somatic genetic abnormalities in these parathyroid carcinomas have never been detected. In this paper, we aimed to describe the clinical and molecular characterization of a parathyroid carcinoma identified in a patient with MEN1. A 60-year-old man was diagnosed with primary hyperparathyroidism during the postoperative period of lung carcinoid surgery. Serum calcium and parathyroid hormone levels were 15.0 mg/dL (8.4-10.2) and 472 pg/mL (12-65), respectively. The patient underwent parathyroid surgery, and histological findings were consistent with parathyroid carcinoma. Analysis of the MEN1 gene by next-generation sequencing (NGS) identified a novel germline heterozygous nonsense pathogenic variant (c.978C>A; p.(Tyr326*)), predicted to encode a truncated protein. Genetic analysis of the parathyroid carcinoma revealed a c.307del, p.(Leu103Cysfs*16) frameshift truncating somatic MEN1 variant in the MEN1 gene, which is consistent with MEN1 tumor-suppressor role, confirming its involvement in parathyroid carcinoma etiology. Genetic analysis of CDC73, GCM2, TP53, RB1, AKT1, MTOR, PIK3CA and CCND1 genes in the parathyroid carcinoma DNA did not detect any somatic mutations. To our knowledge, this is the first report of a PC case presenting both germline (first-hit) and somatic (second-hit) inactivation of the MEN1 gene.

An unusual familial Xp22.12 microduplication including EIF1AX: A novel candidate dosage-sensitive gene for premature ovarian insufficiency

We report on the results of array-CGH and Whole exome sequencing (WES) studies carried out in a Tunisian family with 46,XX premature ovarian insufficiency (POI). This study has led to the identification of a familial Xp22.12 tandem duplication with a size of 559.4 kb, encompassing only three OMIM genes (RPS6KA3, SH3KBP1and EIF1AX), and a new heterozygous variant in SPIDR gene: NM_001080394.3:c.1845_1853delTATAATTGA (p.Ile616_Asp618del) segregating with POI. Increased mRNA expression levels were detected for SH3KBP1 and EIF1AX, while a normal transcript level for RPS6KA3 was detected in the three affected family members, explaining the absence of intellectual disability (ID). To the best of our knowledge, this is the first duplication involving the Xp22.12 region, reported in a family without ID, but rather with secondary amenorrhea (SA) and female infertility. As EIF1AX is a regulatory gene escaping X-inactivation, which has an extreme dosage sensitivity and highly expressed in the ovary, we suggest that this gene might be a candidate gene for ovarian function. Homozygous nonsense pathogenic variants of SPIDR gene have been reported in familial cases in POI. It has been suggested that chromosomal instability associated with SPIDR molecular defects supports the role of SPIDR protein in double-stranded DNA damage repair in vivo in humans and its causal role in POI. In this family, the variant (p.Ile616_Asp618del), present in a heterozygous state, is located in the domain that interacts with BLM and might disrupt the BLM binding ability of SPIDR protein. These findings strengthen the hypothesis that the additional effect of this variant could lead to POI in this family. Although the work represents the first evidence that EIF1AX duplication might be responsible for POI through its over-expression, further functional studies are needed to clarify and prove EIF1AX involvement in POI phenotype.

Childhood-Onset Choreo-Dystonia Due to a Recurrent Novel Homozygous Nonsense HPCA Variant: Case Series and Literature Review.

Biallelic variants in HPCA were linked to isolated dystonia (formerly DYT2) in 2015. Since then, the clinical spectrum of HPCA-related disorder has expanded up to including a complex syndrome encompassing neurodevelopmental delay, generalized dystonia with bulbar involvement, and infantile seizures. We report four individuals with a new phenotype of childhood-onset choreo-dystonia belonging to two unrelated Iranian pedigrees and harboring a novel homozygous nonsense pathogenic variant NM_002143.3:c.49C>T p.(Arg17*) in HPCA. Although the families are both Iranian, haplotype analysis of the exome data did not reveal a founder effect of the variant. A systematic review of articles on HPCA and dystonia published since the disease gene discovery (PubMed; search on July 09, 2022; search strategy "HPCA AND dystonia", "HPCA AND movement disorder", "hippocalcin AND dystonia", and "hippocalcin AND movement disorder"; no language restriction) resulted in 18 references reporting 10 cases from six families. HPCA-related dystonia was isolated or in various combinations with neurodevelopmental delay, intellectual disability, seizures, cognitive decline, and psychiatric comorbidity. Onset of dystonia ranged from infancy to early adulthood. Dystonia started in the limbs or neck and became generalized in most cases. Brain MRI was unremarkable in nearly all cases where performed. There was poor or no response to common antidystonic medications in most cases. Our case series expands the pheno-genotypic spectrum of HPCA-related disorder by describing childhood-onset choreo-dystonia as a new phenotype, reporting on a recurrent novel pathogenic nonsense variant in HPCA, and suggesting that exon 2 of HPCA might be a mutational hotspot.

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.

Expanding the phenotype of SPARC-related osteogenesis imperfecta: clinical findings in two patients with pathogenic variants in SPARC and literature review

BackgroundSecreted protein, acidic, cysteine rich (SPARC)-related osteogenesis imperfecta (OI), also referred to as OI type XVII, was first described in 2015, since then there has been only one further report...

Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report

BackgroundAtaxia-telangiectasia is a rare autosomal recessive, neurodegenerative disorder caused by alterations in the ATM gene. The majority of ATM pathogenic variants are frameshift or nonsense variants which are predicted to truncate the whole ATM protein. Herein, we report on an ataxia telangiectasia child with atypical phenotype who was identified as compound heterozygous for two ATM variants involving a previously described pathogenic single nucleotide variation (SNV) and a novel copy number variation (CNV).Case presentationA 6-year-old boy presented with delayed development and oculomotor apraxia. Brain magnetic resonance imaging showed interval development of mild atrophy in the cerebellum. Serum alpha fetoprotein level was in normal range. Next-generation sequencing and single-nucleotide polymorphism array tests were performed. Next-generation sequencing revealed a heterozygous nonsense pathogenic variant in ATM, c.742C > T (p.Arg248Ter) inherited from the father. Single-nucleotide polymorphism array revealed a compound heterozygous CNV, arr[GRCh37] 11q22.3(10851766–108183226) × 1, 31460 bp (exons 24–40 deletion of ATM) inherited from the mother, which was validated by reverse transcription-polymerase chain reaction analysis (RT-PCR). We demonstrated that this variant (NM_000051.4:c.3403_6006del) generated a product of in-frame deletion of exon 24–40 of ATM (p.Ser1135_Gln2002del).ConclusionsThe compound heterozygosity for ATM variants involving a previously described pathogenic SNV and a novel CNV may be associated with the atypical clinical manifestations. This clinical report extends the genetic and phenotypic spectrum of ATM pathogenic variants in atypical ataxia-telangiectasia, thus making implementation of advanced analysis beyond the routine next-generation sequencing an important consideration in diagnosis and rehabilitation services for children with ataxia-telangiectasia.

Implications of targeted next-generation sequencing for bladder cancer: report of four cases

BackgroundBladder cancer is considered heterogeneous diseases with two major subgroups: non-muscle- invasive bladder cancer (NMIBC) and muscle invasive bladder cancer (MIBC). It is a major healthcare problem, and it is one of the leading causes of mortality worldwide. Genetic mutations are not only a cause for carcinogenesis but are also a way for treatment strategy. The present study aimed to investigate breast cancer (BRCA genes) tumor suppressor gene mutations in bladder cancer tissue and combined blood samples for patients who developed secondary tumor after or during trimodal therapy. Fresh tissue samples and their matched blood samples were collected from four patients with bladder cancer. The objective regions for the examined genes (BRCA1 and BRCA2) were sequenced using next-generation sequencing (NGS); generated BAM files were uploaded to the cloud-based Ionreporter server, and the Oncomine BRCA-specific plugin was used to analyze the paired normal and tumor sample for each patient using the default plugin parameters. ResultsIntronic BRCA1 mutation c.5050-104 C >T was reported among the four investigated bladder cancer patients, and three somatic mutations were reported as follows: two of them were found to be benign rs1064793056 and rs28897679 on the Clinivar database and one nonsense pathogenic variant rs80357006. BRCA 2 gene mutation reported an exonic synonymous mutation rs397507876 in the tissue and germline DNA. Patients were treated with trimodal; however, three bladder cancer patients who reported BRCA mutations developed secondary tumors. ConclusionIdentification of mutational BRCA changes in bladder cancer is a promising marker for better treatment strategy. Further studies are encouraged on a large cohort of bladder cancer patients to confirm our findings.

Incidence and Therapeutic Implications of Germline TP53 Mutations in Hypodiploid Childhood Acute Lymphoblastic Leukemia: A Retrospective Analysis of the Italian Cohort

Background. Hypodiploid Acute Lymphoblastic Leukemia (ALL) is a rare subtype of childhood ALL known to be associated with a poor prognosis. Currently, intensive chemotherapy and haematopoietic stem cell transplantation are recommended as the main therapeutic strategy for these patients. Previous studies showed that low-hypodiploid ALL frequently carry TP53 variants, the majority of which are germline mutations. This finding suggests that hypodiploid ALL may be a manifestation of underlying Li-Fraumeni syndrome, with an associated high risk for secondary tumors. We analyzed TP53 variants in the Italian cohort of hypodiploid pediatric ALL patients diagnosed between 2000 and 2019, to explore frequency and characteristics, as well as the potential role of germline variants in the therapeutic strategy. Patients were treated according to the AIEOP-BFM ALL2000 (n=16), ALL2009 (n=16) and ALL2017 (n=8) protocols. Methods. We performed a targeted Next Generation Sequencing (NGS) Nextera Flex DNA panel of 40 genes, including TP53, in a retrospective series of hypodiploid paediatric ALL Italian patients enrolled in four nationwide frontline protocols. Ploidy was defined based on DNA index (DNAi) and/or cytogenetics/FISH, and cases with DNAi<0.8 were included in this study. Only TP53 variants with VF >5% and coverage 500X were considered. Bioinformatics analysis has been carried out by Sophia DDM software. NGS has been performed both in disease (hematopoietic) and germline (remission or buccal brush) tissues samples. Results. Nineteen TP53 variants were observed in 20/40 (50%) hypodiploid ALL patients, with 19/20 being low-hypodiploid ALL cases (DNAi between 0,6 and 0,8); 13/19 TP53 variants were known to be pathogenic whereas 6/19 were classified as Variant of Unknown Significance (VUS). Considering the VUS variants, 3/6 were missense, 1/6 frameshift and 2/6 in-frame ins/del. Notably, 13 patients out of 20 (65%) were found to carry a germline variant, while 5 patients presented a somatic variant; in 2 cases the remission sample was not available, but the VF<20% was indicative of a somatic variant. Among the germline variants, 1 was found to be a germline mosaicism, presenting a nonsense pathogenic TP53 variant both in remission (VF 10%) and buccal brush sample at remission (VF 8.5%). 16/19 variants reside in the p53 core DNA binding domain, known to be a fundamental site that mediates the transcription of p53 regulated genes, where most of the pathogenic mutations in cancer cells occur. The 3 variants outside the DNA binding domain were 1 nonsense, 1 frameshift and 1 missense, and were localized in the nuclear localization signal region (NLS) or in the oligomerization domain (OD). Considering the 32 patients with at least 5 years of follow-up, EFS was not significantly different between TP53 wild type (47.1% ± 12.1) vs TP53 variant (51.9% ± 17,8) subgroups. According to MRD stratification criteria, the patients carrying a TP53 variant were classified as medium risk in 14/20, standard risk in 5/20 and HR in 1 case, not statistically different from TP53 wild type. Collection of data on secondary neoplasms in patients and their relatives in ongoing. Conclusion. Our data represent the largest low hypodiploid patient cohort tested so far, confirming the high frequency of deleterious TP53 mutations. Mutational testing of TP53 in patients with hypodiploid ALL is warranted, in order to ensure a proper genetic counseling for patients with germline mutations and their families, with tailored clinical surveillance (according to Li-Fraumeni Syndrome guidelines). The best therapeutic regimen for hypodiploid patients is still a matter of debate, with MRD at the end of induction and TP53 germline mutations potentially indicating a highest relevance in the indication to hematopoietic stem cell transplantation. Chemotherapy-only treatment could be indicated for MRD-low patients and HSCT for MRD-High, potentially considering a reduced conditioning regimen for TP53 mutated cases. Disclosures Locatelli: Amgen: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Novartis: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Bellicum Pharmaceutical: Membership on an entity's Board of Directors or advisory committees; Miltenyi: Speakers Bureau; Medac: Speakers Bureau; Jazz Pharmaceeutical: Speakers Bureau. Rizzari:Sobi: Consultancy, Other: Advisory Board.

Genetic spectrum of retinal dystrophies in Tunisia

We report the molecular basis of the largest Tunisian cohort with inherited retinal dystrophies (IRD) reported to date, identify disease-causing pathogenic variants and describe genotype–phenotype correlations. A subset of 26 families from a cohort of 73 families with clinical diagnosis of autosomal recessive IRD (AR-IRD) excluding Usher syndrome was analyzed by whole exome sequencing and autozygosity mapping. Causative pathogenic variants were identified in 50 families (68.4%), 42% of which were novel.The most prevalent pathogenic variants were observed in ABCA4 (14%) and RPE65, CRB1 and CERKL (8% each). 26 variants (8 novel and 18 known) in 19 genes were identified in 26 families (14 missense substitutions, 5 deletions, 4 nonsense pathogenic variants and 3 splice site variants), with further allelic heterogeneity arising from different pathogenic variants in the same gene. The most common phenotype in our cohort is retinitis pigmentosa (23%) and cone rod dystrophy (23%) followed by Leber congenital amaurosis (19.2%). We report the association of new disease phenotypes. This research was carried out in Tunisian patients with IRD in order to delineate the genetic population architecture.

Dento-osseous anomalies in patients with familial adenomatous polyposis: A follow-up study.

The aim of this longitudinal study was to characterize the dento-osseous phenotype of eleven familial adenomatous polyposis (FAP) patients and twenty-two family members from four Brazilian families who were followed over nine years and to investigate adenomatous polyposis coli (APC) gene variants using a targeted next-generation sequencing approach. Medical and dental history, oral examination, and panoramic radiography were performed to diagnose and follow up the dento-osseous anomalies. The anomalies were evaluated following the validated diagnostic tool dental panoramic radiographic score (DPRS), a system developed for high-risk FAP patients. Patients diagnosed with dento-osseous anomalies underwent cone-beam computed tomography. For genetic analysis, DNA was isolated from patients' saliva. Dento-osseous anomalies were identified in ten of the eleven FAP patients by panoramic radiograph evaluation. DPRS ≥ 7 (significant changes) was found in 81.8% (9/11) of FAP patients. The follow-up showed an increase in osseous jaw lesions in two young patients during adolescence. Dento-osseous anomalies were not found in non-FAP patients. A novel heterozygous nonsense pathogenic variant in APC exon 5 (c.481C > T; p.Gln161*) was identified in family 2, and a heterozygous splice-site pathogenic variant was identified in family 1 (c.532-1G > A). Our study expands the mutation spectrum of the APC gene and provides evidence that dento-osseous screening by imaging is a putative tool for early diagnosis of FAP. Also, the detection of dento-osseous anomalies in young patients with increasing osseous lesions during adolescence highlights the need for dental follow-up of high-risk FAP children. Dental radiographs are important for the screening and the follow-up of dento-osseous anomalies associated with FAP. It can also contribute to the early diagnosis of the disease.

Identification of c.1531C>T Pathogenic Variant in the CDH1 Gene as a Novel Germline Mutation of Hereditary Diffuse Gastric Cancer.

Germline pathogenic variants in the CDH1 gene are a well-established cause of hereditary diffuse gastric cancer (HDGC) syndrome. The aim of this study was to characterize CDH1 mutations associated with HDGC from Chile, a country with one of the highest incidence and mortality rates in the world for gastric cancer (GC). Here, we prospectively include probands with family history/early onset of diffuse-type of GC. The whole coding sequence of the CDH1 gene was sequenced from genomic DNA in all patients, and a multidisciplinary team managed each family member with a pathogenic sequence variant. Thirty-six cases were included (median age 44 years/male 50%). Twenty-seven (75%) patients had diffuse-type GC at ≤50 years of age and 19 (53%) had first or second-degree family members with a history of HDGC. Two cases (5.5%) carried a non-synonymous germline sequence variant in the CDH1 gene: (a) The c.88C>A missense variant was found in a family with three diffuse-type GC cases; and (b) c.1531C>T a nonsense pathogenic variant was identified in a 22-year-old proband with no previous family history of HDGC. Of note, six family members carry the same nonsense pathogenic variant. Prophylactic gastrectomy in the proband’s sister revealed stage I signet-ring cell carcinoma. The finding of 1531C>T pathogenic variant in the CDH1 in proband with no previous family history of HDGC warrants further study to uncover familial clustering of disease in CDH1 negative patients. This finding may be particularly relevant in high incidence countries, such as the case in this report.