Pub Date : 2024-06-01DOI: 10.1038/s41431-024-01643-6
Andrea Gazzin, Federico Fornari, Marcello Niceta, Chiara Leoni, Maria Lisa Dentici, Diana Carli, Anna Maria Villar, Giulio Calcagni, Elena Banaudi, Stefania Massuras, Simona Cardaropoli, Elena Airulo, Paola Daniele, Emanuele Monda, Giuseppe Limongelli, Chiara Riggi, Giuseppe Zampino, Maria Cristina Digilio, Alessandro De Luca, Marco Tartaglia, Giovanni Battista Ferrero, Alessandro Mussa
Hypertrophic cardiomyopathy (HCM) is the major contributor to morbidity and mortality in Noonan syndrome (NS). Gain-of-function variants in RAF1 are associated with high prevalence of HCM. Among these, NM_002880.4:c.770C > T, NP_002871.1:p.(Ser257Leu) accounts for approximately half of cases and has been reported as associated with a particularly severe outcome. Nevertheless, comprehensive studies on cases harboring this variant are missing. To precisely define the phenotype associated to the RAF1:c.770C > T, variant, an observational retrospective analysis on patients carrying the c.770C > T variant was conducted merging 17 unpublished patients and literature-derived ones. Data regarding prenatal findings, clinical features and cardiac phenotypes were collected to provide an exhaustive description of the associated phenotype. Clinical information was collected in 107 patients. Among them, 92% had HCM, mostly diagnosed within the first year of life. Thirty percent of patients were preterm and 47% of the newborns was admitted in a neonatal intensive care unit, mainly due to respiratory complications of HCM and/or pulmonary arterial hypertension. Mortality rate was 13%, mainly secondary to HCM-related complications (62%) at the average age of 7.5 months. Short stature had a prevalence of 91%, while seizures and ID of 6% and 12%, respectively. Two cases out of 75 (3%) developed neoplasms. In conclusion, patients with the RAF1:c.770C > T pathogenic variant show a particularly severe phenotype characterized by rapidly progressive neonatal HCM and high mortality rate suggesting the necessity of careful monitoring and early intervention to prevent or slow down the progression of HCM.
肥厚型心肌病（HCM）是导致努南综合征（NS）发病和死亡的主要原因。RAF1 的功能增益变异与 HCM 的高发病率有关。其中，NM_002880.4:c.770C > T, NP_002871.1:p.(Ser257Leu)约占半数病例，有报道称这与特别严重的预后有关。然而，目前还没有对携带这种变异的病例进行全面研究。为了准确定义与 RAF1:c.770C > T 变异相关的表型，我们对携带 c.770C > T 变异的患者进行了观察性回顾分析，合并了 17 例未发表的患者和文献中的数据。收集了有关产前发现、临床特征和心脏表型的数据，以提供相关表型的详尽描述。共收集了 107 例患者的临床信息。其中，92% 的患者患有 HCM，大部分是在出生后第一年内确诊的。30%的患者为早产儿，47%的新生儿住进了新生儿重症监护室，主要原因是HCM和/或肺动脉高压引起的呼吸系统并发症。平均年龄为 7.5 个月时，死亡率为 13%，主要继发于 HCM 相关并发症（62%）。身材矮小的发病率为 91%，而癫痫和 ID 的发病率分别为 6% 和 12%。75例患者中有2例（3%）出现肿瘤。总之，RAF1:c.770C > T 致病变异患者表现出特别严重的表型，其特点是新生儿 HCM 进展迅速，死亡率高，这表明有必要进行仔细监测和早期干预，以预防或减缓 HCM 的进展。
{"title":"Defining the variant-phenotype correlation in patients affected by Noonan syndrome with the RAF1:c.770C>T p.(Ser257Leu) variant","authors":"Andrea Gazzin, Federico Fornari, Marcello Niceta, Chiara Leoni, Maria Lisa Dentici, Diana Carli, Anna Maria Villar, Giulio Calcagni, Elena Banaudi, Stefania Massuras, Simona Cardaropoli, Elena Airulo, Paola Daniele, Emanuele Monda, Giuseppe Limongelli, Chiara Riggi, Giuseppe Zampino, Maria Cristina Digilio, Alessandro De Luca, Marco Tartaglia, Giovanni Battista Ferrero, Alessandro Mussa","doi":"10.1038/s41431-024-01643-6","DOIUrl":"10.1038/s41431-024-01643-6","url":null,"abstract":"Hypertrophic cardiomyopathy (HCM) is the major contributor to morbidity and mortality in Noonan syndrome (NS). Gain-of-function variants in RAF1 are associated with high prevalence of HCM. Among these, NM_002880.4:c.770C > T, NP_002871.1:p.(Ser257Leu) accounts for approximately half of cases and has been reported as associated with a particularly severe outcome. Nevertheless, comprehensive studies on cases harboring this variant are missing. To precisely define the phenotype associated to the RAF1:c.770C > T, variant, an observational retrospective analysis on patients carrying the c.770C > T variant was conducted merging 17 unpublished patients and literature-derived ones. Data regarding prenatal findings, clinical features and cardiac phenotypes were collected to provide an exhaustive description of the associated phenotype. Clinical information was collected in 107 patients. Among them, 92% had HCM, mostly diagnosed within the first year of life. Thirty percent of patients were preterm and 47% of the newborns was admitted in a neonatal intensive care unit, mainly due to respiratory complications of HCM and/or pulmonary arterial hypertension. Mortality rate was 13%, mainly secondary to HCM-related complications (62%) at the average age of 7.5 months. Short stature had a prevalence of 91%, while seizures and ID of 6% and 12%, respectively. Two cases out of 75 (3%) developed neoplasms. In conclusion, patients with the RAF1:c.770C > T pathogenic variant show a particularly severe phenotype characterized by rapidly progressive neonatal HCM and high mortality rate suggesting the necessity of careful monitoring and early intervention to prevent or slow down the progression of HCM.","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":"32 8","pages":"964-971"},"PeriodicalIF":3.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141186185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-01DOI: 10.1038/s41431-024-01642-7
Maria Lisa Dentici, Marcello Niceta, Francesca Romana Lepri, Cecilia Mancini, Manuela Priolo, Adeline Alice Bonnard, Camilla Cappelletti, Chiara Leoni, Andrea Ciolfi, Simone Pizzi, Viviana Cordeddu, Cesare Rossi, Marco Ferilli, Mafalda Mucciolo, Vito Luigi Colona, Christine Fauth, Melissa Bellini, Giacomo Biasucci, Lorenzo Sinibaldi, Silvana Briuglia, Andrea Gazzin, Diana Carli, Luigi Memo, Eva Trevisson, Concetta Schiavariello, Maria Luca, Antonio Novelli, Caroline Michot, Anne Sweertvaegher, David Germanaud, Emanuela Scarano, Alessandro De Luca, Giuseppe Zampino, Martin Zenker, Alessandro Mussa, Bruno Dallapiccola, Helene Cavé, Maria Cristina Digilio, Marco Tartaglia
Pathogenic, largely truncating variants in the ETS2 repressor factor (ERF) gene, encoding a transcriptional regulator negatively controlling RAS-MAPK signaling, have been associated with syndromic craniosynostosis involving various cranial sutures and Chitayat syndrome, an ultrarare condition with respiratory distress, skeletal anomalies, and facial dysmorphism. Recently, a single patient with craniosynostosis and a phenotype resembling Noonan syndrome (NS), the most common disorder among the RASopathies, was reported to carry a de novo loss-of-function variant in ERF. Here, we clinically profile 26 individuals from 15 unrelated families carrying different germline heterozygous variants in ERF and showing a phenotype reminiscent of NS. The majority of subjects presented with a variable degree of global developmental and/or language delay. Their shared facial features included absolute/relative macrocephaly, high forehead, hypertelorism, palpebral ptosis, wide nasal bridge, and low-set/posteriorly angulated ears. Stature was below the 3rd centile in two-third of the individuals, while no subject showed typical NS cardiac involvement. Notably, craniosynostosis was documented only in three unrelated individuals, while a dolichocephalic aspect of the skull in absence of any other evidence supporting a premature closing of sutures was observed in other 10 subjects. Unilateral Wilms tumor was diagnosed in one individual. Most cases were familial, indicating an overall low impact on fitness. Variants were nonsense and frameshift changes, supporting ERF haploinsufficiency. These findings provide evidence that heterozygous loss-of-function variants in ERF cause a “RASopathy” resembling NS with or without craniosynostosis, and allow a first dissection of the molecular circuits contributing to MAPK signaling pleiotropy.
{"title":"Loss-of-function variants in ERF are associated with a Noonan syndrome-like phenotype with or without craniosynostosis","authors":"Maria Lisa Dentici, Marcello Niceta, Francesca Romana Lepri, Cecilia Mancini, Manuela Priolo, Adeline Alice Bonnard, Camilla Cappelletti, Chiara Leoni, Andrea Ciolfi, Simone Pizzi, Viviana Cordeddu, Cesare Rossi, Marco Ferilli, Mafalda Mucciolo, Vito Luigi Colona, Christine Fauth, Melissa Bellini, Giacomo Biasucci, Lorenzo Sinibaldi, Silvana Briuglia, Andrea Gazzin, Diana Carli, Luigi Memo, Eva Trevisson, Concetta Schiavariello, Maria Luca, Antonio Novelli, Caroline Michot, Anne Sweertvaegher, David Germanaud, Emanuela Scarano, Alessandro De Luca, Giuseppe Zampino, Martin Zenker, Alessandro Mussa, Bruno Dallapiccola, Helene Cavé, Maria Cristina Digilio, Marco Tartaglia","doi":"10.1038/s41431-024-01642-7","DOIUrl":"10.1038/s41431-024-01642-7","url":null,"abstract":"Pathogenic, largely truncating variants in the ETS2 repressor factor (ERF) gene, encoding a transcriptional regulator negatively controlling RAS-MAPK signaling, have been associated with syndromic craniosynostosis involving various cranial sutures and Chitayat syndrome, an ultrarare condition with respiratory distress, skeletal anomalies, and facial dysmorphism. Recently, a single patient with craniosynostosis and a phenotype resembling Noonan syndrome (NS), the most common disorder among the RASopathies, was reported to carry a de novo loss-of-function variant in ERF. Here, we clinically profile 26 individuals from 15 unrelated families carrying different germline heterozygous variants in ERF and showing a phenotype reminiscent of NS. The majority of subjects presented with a variable degree of global developmental and/or language delay. Their shared facial features included absolute/relative macrocephaly, high forehead, hypertelorism, palpebral ptosis, wide nasal bridge, and low-set/posteriorly angulated ears. Stature was below the 3rd centile in two-third of the individuals, while no subject showed typical NS cardiac involvement. Notably, craniosynostosis was documented only in three unrelated individuals, while a dolichocephalic aspect of the skull in absence of any other evidence supporting a premature closing of sutures was observed in other 10 subjects. Unilateral Wilms tumor was diagnosed in one individual. Most cases were familial, indicating an overall low impact on fitness. Variants were nonsense and frameshift changes, supporting ERF haploinsufficiency. These findings provide evidence that heterozygous loss-of-function variants in ERF cause a “RASopathy” resembling NS with or without craniosynostosis, and allow a first dissection of the molecular circuits contributing to MAPK signaling pleiotropy.","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":"32 8","pages":"954-963"},"PeriodicalIF":3.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141186213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
STAC3 disorder, or Native American myopathy, is characterised by congenital myopathy, hypotonia, musculoskeletal and palatal anomalies, and susceptibility to malignant hyperthermia. A STAC3 c.851 G > C (p.Trp284Ser) pathogenic variant, common in the Lumbee Native American tribe, has been identified in other populations worldwide, including patients of African ancestry. We report on the frequency of STAC3 c.851 G > C in a cohort of 127 patients presenting with congenital hypotonia that tested negative for spinal muscular atrophy and/or Prader-Willi syndrome. We present a clinical retrospective, descriptive review on 31 Southern African patients homozygous for STAC3 c.851 G > C. The frequencies of various phenotypic characteristics were calculated. In total, 25/127 (20%) laboratory-based samples were homozygous for STAC3 c.851 G > C. A carrier rate of 1/56 and a predicted birth rate of 1/12 500 was estimated from a healthy cohort. A common haplotype spanning STAC3 was identified in four patients. Of the clinical group, 93% had a palatal abnormality, 52% a spinal anomaly, 59% had talipes equinovarus deformity/deformities, 38% had arthrogryposis multiplex congenita, and 22% had a history suggestive of malignant hyperthermia. The novel finding that STAC3 disorder is a common African myopathy has important clinical implications for the diagnosis, treatment and genetic counselling of individuals, with neonatal and/or childhood hypotonia with or without arthrogryposis multiplex congenita, and their families. The spread of this variant worldwide and the allele frequency higher in the African/African-American ancestry than the Admixed Americans, strongly indicates that the STAC3 c.851 G > C variant has an African origin which may be due to an ancient mutation with migration and population bottlenecks.
STAC3 障碍或美国原住民肌病的特征是先天性肌病、肌张力低下、肌肉骨骼和腭畸形，以及对恶性高热的易感性。STAC3 c.851 G > C (p.Trp284Ser)致病变体常见于伦比美洲原住民部落，已在全球其他人群中发现，包括非洲裔患者。我们报告了一组 127 例先天性肌张力低下患者中 STAC3 c.851 G > C 的频率，这些患者的脊髓性肌萎缩症和/或普拉德-威利综合征检测结果均为阴性。我们对 31 名同源性 STAC3 c.851 G > C 的南部非洲患者进行了临床回顾性描述性研究。我们计算了各种表型特征的频率。共有 25/127 份（20%）基于实验室的样本为 STAC3 c.851 G > C 的同源基因。根据健康人群的估计，携带率为 1/56，预测出生率为 1/12 500。在四名患者中发现了跨越 STAC3 的共同单倍型。在临床组中，93%的患者有腭畸形，52%的患者有脊柱异常，59%的患者有马蹄内翻足畸形，38%的患者有先天性关节发育不良，22%的患者有恶性高热病史。STAC3障碍是一种常见的非洲肌病，这一新颖发现对新生儿和/或儿童肌张力低下伴或不伴先天性多关节发育不良患者及其家庭的诊断、治疗和遗传咨询具有重要的临床意义。该变异在全球范围内的传播以及非洲/非裔美国人血统中的等位基因频率高于混血美国人，有力地表明 STAC3 c.851 G > C 变异起源于非洲，可能是由于迁移和人口瓶颈造成的古老变异。
{"title":"STAC3 disorder: a common cause of congenital hypotonia in Southern African patients.","authors":"Fahmida Essop, Bronwyn Dillon, Felicity Mhlongo, Louisa Bhengu, Thirona Naicker, Lindsay Lambie, Liani Smit, Karen Fieggen, Anneline Lochan, Jessica Dawson, Phelelani Mpangase, Marc Hauptfleisch, Gail Scher, Odirile Tabane, Marelize Immelman, Michael Urban, Amanda Krause","doi":"10.1038/s41431-024-01644-5","DOIUrl":"10.1038/s41431-024-01644-5","url":null,"abstract":"<p><p>STAC3 disorder, or Native American myopathy, is characterised by congenital myopathy, hypotonia, musculoskeletal and palatal anomalies, and susceptibility to malignant hyperthermia. A STAC3 c.851 G > C (p.Trp284Ser) pathogenic variant, common in the Lumbee Native American tribe, has been identified in other populations worldwide, including patients of African ancestry. We report on the frequency of STAC3 c.851 G > C in a cohort of 127 patients presenting with congenital hypotonia that tested negative for spinal muscular atrophy and/or Prader-Willi syndrome. We present a clinical retrospective, descriptive review on 31 Southern African patients homozygous for STAC3 c.851 G > C. The frequencies of various phenotypic characteristics were calculated. In total, 25/127 (20%) laboratory-based samples were homozygous for STAC3 c.851 G > C. A carrier rate of 1/56 and a predicted birth rate of 1/12 500 was estimated from a healthy cohort. A common haplotype spanning STAC3 was identified in four patients. Of the clinical group, 93% had a palatal abnormality, 52% a spinal anomaly, 59% had talipes equinovarus deformity/deformities, 38% had arthrogryposis multiplex congenita, and 22% had a history suggestive of malignant hyperthermia. The novel finding that STAC3 disorder is a common African myopathy has important clinical implications for the diagnosis, treatment and genetic counselling of individuals, with neonatal and/or childhood hypotonia with or without arthrogryposis multiplex congenita, and their families. The spread of this variant worldwide and the allele frequency higher in the African/African-American ancestry than the Admixed Americans, strongly indicates that the STAC3 c.851 G > C variant has an African origin which may be due to an ancient mutation with migration and population bottlenecks.</p>","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141186226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-31DOI: 10.1038/s41431-024-01637-4
German Demidov, Steven Laurie, Annalaura Torella, Giulio Piluso, Marcello Scala, Manuela Morleo, Vincenzo Nigro, Holm Graessner, Siddharth Banka, Solve-RD consortium, Katja Lohmann, Stephan Ossowski
Structural variants (SVs), including large deletions, duplications, inversions, translocations, and more complex events have the potential to disrupt gene function resulting in rare disease. Nevertheless, current pipelines and clinical decision support systems for exome sequencing (ES) tend to focus on small alterations such as single nucleotide variants (SNVs) and insertions-deletions shorter than 50 base pairs (indels). Additionally, detection and interpretation of large copy-number variants (CNVs) are frequently performed. However, detection of other types of SVs in ES data is hampered by the difficulty of identifying breakpoints in off-target (intergenic or intronic) regions, which makes robust identification of SVs challenging. In this paper, we demonstrate the utility of SV calling in ES resulting in a diagnostic yield of 0.4% (23 out of 5825 probands) for a large cohort of unsolved patients collected by the Solve-RD consortium. Remarkably, 8 out of 23 pathogenic SV were not found by comprehensive read-depth-based CNV analysis, resulting in a 0.13% increased diagnostic value.
{"title":"Structural variant calling and clinical interpretation in 6224 unsolved rare disease exomes","authors":"German Demidov, Steven Laurie, Annalaura Torella, Giulio Piluso, Marcello Scala, Manuela Morleo, Vincenzo Nigro, Holm Graessner, Siddharth Banka, Solve-RD consortium, Katja Lohmann, Stephan Ossowski","doi":"10.1038/s41431-024-01637-4","DOIUrl":"10.1038/s41431-024-01637-4","url":null,"abstract":"Structural variants (SVs), including large deletions, duplications, inversions, translocations, and more complex events have the potential to disrupt gene function resulting in rare disease. Nevertheless, current pipelines and clinical decision support systems for exome sequencing (ES) tend to focus on small alterations such as single nucleotide variants (SNVs) and insertions-deletions shorter than 50 base pairs (indels). Additionally, detection and interpretation of large copy-number variants (CNVs) are frequently performed. However, detection of other types of SVs in ES data is hampered by the difficulty of identifying breakpoints in off-target (intergenic or intronic) regions, which makes robust identification of SVs challenging. In this paper, we demonstrate the utility of SV calling in ES resulting in a diagnostic yield of 0.4% (23 out of 5825 probands) for a large cohort of unsolved patients collected by the Solve-RD consortium. Remarkably, 8 out of 23 pathogenic SV were not found by comprehensive read-depth-based CNV analysis, resulting in a 0.13% increased diagnostic value.","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":"32 8","pages":"998-1004"},"PeriodicalIF":3.7,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11291474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141183744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-30DOI: 10.1038/s41431-024-01641-8
Lisa G. Riley, Subrata Sabui, Hamid M. Said, Aram Niaz, Katta M. Girisha, Periyasamy Radhakrishnan, Sheela Nampoothiri, Dhanya Yesodharan, Tatjana Kilo, Janine Smith, Rachel S. H. Wong, Manoj P. Menezes, Sachin Gupta, Sandra T. Cooper, Shanti Balasubramaniam
The sodium-dependent multivitamin transporter encoded by SLC5A6 is responsible for uptake of biotin, pantothenic acid, and α-lipoic acid. Thirteen individuals from eight families are reported with pathogenic biallelic SLC5A6 variants. Phenotype ranges from multisystem metabolic disorder to childhood-onset peripheral motor neuropathy. We report three additional affected individuals with biallelic SLC5A6 variants. In Family A, a male proband (AII:1) presenting in early childhood with gross motor regression, motor axonal neuropathy, recurrent cytopenia and infections, and failure to thrive was diagnosed at 12 years of age via genome sequencing (GS) with a paternal NM_021095.4:c.393+2T>C variant and a maternal c.1285A>G p.(Ser429Gly) variant. An uncle with recurrent cytopenia and peripheral neuropathy was subsequently found to have the same genotype. We also report an unrelated female with peripheral neuropathy homozygous for the c.1285A>G p.(Ser429Gly) recurrent variant identified in seven reported cases, including this study. RT-PCR studies on blood mRNA from AII:1 showed c.393+2T>C caused mis-splicing with all canonically spliced transcripts in AII:1 containing the c.1285A>G variant. SLC5A6 mRNA expression in AII:1 fibroblasts was ~50% of control levels, indicative of nonsense-mediated decay of mis-spliced transcripts. Biotin uptake studies on AII:1 fibroblasts, expressing the p.(Ser429Gly) variant, showed an ~90% reduction in uptake compared to controls. Targeted treatment of AII:1 with biotin, pantothenic acid, and lipoic acid resulted in clinical improvement. Health Economic analyses showed implementation of GS as an early investigation could have saved $ AUD 105,988 and shortened diagnostic odyssey and initiation of treatment by up to 7 years.
{"title":"Genome sequencing enables diagnosis and treatment of SLC5A6 neuropathy","authors":"Lisa G. Riley, Subrata Sabui, Hamid M. Said, Aram Niaz, Katta M. Girisha, Periyasamy Radhakrishnan, Sheela Nampoothiri, Dhanya Yesodharan, Tatjana Kilo, Janine Smith, Rachel S. H. Wong, Manoj P. Menezes, Sachin Gupta, Sandra T. Cooper, Shanti Balasubramaniam","doi":"10.1038/s41431-024-01641-8","DOIUrl":"10.1038/s41431-024-01641-8","url":null,"abstract":"The sodium-dependent multivitamin transporter encoded by SLC5A6 is responsible for uptake of biotin, pantothenic acid, and α-lipoic acid. Thirteen individuals from eight families are reported with pathogenic biallelic SLC5A6 variants. Phenotype ranges from multisystem metabolic disorder to childhood-onset peripheral motor neuropathy. We report three additional affected individuals with biallelic SLC5A6 variants. In Family A, a male proband (AII:1) presenting in early childhood with gross motor regression, motor axonal neuropathy, recurrent cytopenia and infections, and failure to thrive was diagnosed at 12 years of age via genome sequencing (GS) with a paternal NM_021095.4:c.393+2T>C variant and a maternal c.1285A>G p.(Ser429Gly) variant. An uncle with recurrent cytopenia and peripheral neuropathy was subsequently found to have the same genotype. We also report an unrelated female with peripheral neuropathy homozygous for the c.1285A>G p.(Ser429Gly) recurrent variant identified in seven reported cases, including this study. RT-PCR studies on blood mRNA from AII:1 showed c.393+2T>C caused mis-splicing with all canonically spliced transcripts in AII:1 containing the c.1285A>G variant. SLC5A6 mRNA expression in AII:1 fibroblasts was ~50% of control levels, indicative of nonsense-mediated decay of mis-spliced transcripts. Biotin uptake studies on AII:1 fibroblasts, expressing the p.(Ser429Gly) variant, showed an ~90% reduction in uptake compared to controls. Targeted treatment of AII:1 with biotin, pantothenic acid, and lipoic acid resulted in clinical improvement. Health Economic analyses showed implementation of GS as an early investigation could have saved $ AUD 105,988 and shortened diagnostic odyssey and initiation of treatment by up to 7 years.","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":"32 8","pages":"947-953"},"PeriodicalIF":3.7,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141179302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-29DOI: 10.1038/s41431-024-01640-9
Lisa Dive, Anne-Marie Laberge, Lucinda Freeman, Eline M. Bunnik
Reproductive genetic carrier screening (RGCS) allows prospective parents to identify and act upon their chances of having a child with a genetic condition. In deciding which genetic conditions to include in RGCS, severity is often used as a criterion. However, the concept is inherently complex, subjective and multidimensional, and determinations of severity will remain intractably contested. We propose the concept of utility as a criterion for setting the scope of RGCS, and put forward two central arguments for doing so. First, utility is a more appropriate and effective concept as it responds to context and makes an explicit connection between the purpose of RGCS and the value of information obtained for that purpose: namely, to facilitate reproductive decision-making. Utility comprises both clinical and personal utility, and varies according to the availability and accessibility of reproductive options, including pre-implantation genetic testing, prenatal genetic diagnosis, and termination of pregnancy. Second, there are ethical reasons for preferring utility over severity. Utility is a property of the information gleaned from RGCS, while severity is a property of a genetic condition or of an instance of this condition in a person. While consideration of the severity of genetic conditions is not lost when focusing on utility, the need to rely on value judgements regarding the quality of life of people who live with genetic conditions is circumvented. Therefore, utility should replace severity as justification for the inclusion of genetic conditions in RGCS programmes.
{"title":"Beyond severity: utility as a criterion for setting the scope of RGCS","authors":"Lisa Dive, Anne-Marie Laberge, Lucinda Freeman, Eline M. Bunnik","doi":"10.1038/s41431-024-01640-9","DOIUrl":"https://doi.org/10.1038/s41431-024-01640-9","url":null,"abstract":"<p>Reproductive genetic carrier screening (RGCS) allows prospective parents to identify and act upon their chances of having a child with a genetic condition. In deciding which genetic conditions to include in RGCS, severity is often used as a criterion. However, the concept is inherently complex, subjective and multidimensional, and determinations of severity will remain intractably contested. We propose the concept of utility as a criterion for setting the scope of RGCS, and put forward two central arguments for doing so. First, utility is a more appropriate and effective concept as it responds to context and makes an explicit connection between the purpose of RGCS and the value of information obtained for that purpose: namely, to facilitate reproductive decision-making. Utility comprises both clinical and personal utility, and varies according to the availability and accessibility of reproductive options, including pre-implantation genetic testing, prenatal genetic diagnosis, and termination of pregnancy. Second, there are ethical reasons for preferring utility over severity. Utility is a property of the information gleaned from RGCS, while severity is a property of a genetic condition or of an instance of this condition in a person. While consideration of the severity of genetic conditions is not lost when focusing on utility, the need to rely on value judgements regarding the quality of life of people who live with genetic conditions is circumvented. Therefore, utility should replace severity as justification for the inclusion of genetic conditions in RGCS programmes.</p>","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":"46 1","pages":""},"PeriodicalIF":5.2,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141169984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-28DOI: 10.1038/s41431-024-01627-6
Kae R. Whiting, Lonneke Haer-Wigman, Ralph J. Florijn, Ronald van Beek, Machteld M. Oud, Astrid S. Plomp, Camiel J. F. Boon, Hester Y. Kroes, Ronald Roepman
INPP5E encodes inositol polyphosphate-5-phosphatase E, an enzyme involved in regulating the phosphatidylinositol (PIP) makeup of the primary cilium membrane. Pathogenic variants in INPP5E hence cause a variety of ciliopathies: genetic disorders caused by dysfunctional cilia. While the majority of these disorders are syndromic, such as the neuronal ciliopathy Joubert syndrome, in some cases patients will present with an isolated phenotype—most commonly non-syndromic retinitis pigmentosa (RP). Here, we report two novel variants in INPP5E identified in two patients with non-syndromic RP: patient 1 with compound heterozygous variants (c.1516C > T, p.(Q506*), and c.847G > A, p.(A283T)) and patient 2 with a homozygous variant (c.1073C > T, p.(P358L)). To determine whether these variants were causative for the phenotype in the patients, automated ciliary phenotyping of patient-derived dermal fibroblasts was performed for percent ciliation, cilium length, retrograde IFT trafficking, and INPP5E localization. In both patients, a decrease in ciliary length and loss of INPP5E localization in the primary cilia were seen. With these molecular findings, we can confirm functionally that the novel variants in INPP5E are causative for the RP phenotypes seen in both patients. Additionally, this study demonstrates the usefulness of utilizing ciliary phenotyping as an assistant in ciliopathy diagnosis and phenotyping.
{"title":"Utilization of automated cilia analysis to characterize novel INPP5E variants in patients with non-syndromic retinitis pigmentosa","authors":"Kae R. Whiting, Lonneke Haer-Wigman, Ralph J. Florijn, Ronald van Beek, Machteld M. Oud, Astrid S. Plomp, Camiel J. F. Boon, Hester Y. Kroes, Ronald Roepman","doi":"10.1038/s41431-024-01627-6","DOIUrl":"10.1038/s41431-024-01627-6","url":null,"abstract":"INPP5E encodes inositol polyphosphate-5-phosphatase E, an enzyme involved in regulating the phosphatidylinositol (PIP) makeup of the primary cilium membrane. Pathogenic variants in INPP5E hence cause a variety of ciliopathies: genetic disorders caused by dysfunctional cilia. While the majority of these disorders are syndromic, such as the neuronal ciliopathy Joubert syndrome, in some cases patients will present with an isolated phenotype—most commonly non-syndromic retinitis pigmentosa (RP). Here, we report two novel variants in INPP5E identified in two patients with non-syndromic RP: patient 1 with compound heterozygous variants (c.1516C > T, p.(Q506*), and c.847G > A, p.(A283T)) and patient 2 with a homozygous variant (c.1073C > T, p.(P358L)). To determine whether these variants were causative for the phenotype in the patients, automated ciliary phenotyping of patient-derived dermal fibroblasts was performed for percent ciliation, cilium length, retrograde IFT trafficking, and INPP5E localization. In both patients, a decrease in ciliary length and loss of INPP5E localization in the primary cilia were seen. With these molecular findings, we can confirm functionally that the novel variants in INPP5E are causative for the RP phenotypes seen in both patients. Additionally, this study demonstrates the usefulness of utilizing ciliary phenotyping as an assistant in ciliopathy diagnosis and phenotyping.","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":"32 11","pages":"1412-1418"},"PeriodicalIF":3.7,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41431-024-01627-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141161443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-28DOI: 10.1038/s41431-024-01636-5
Holly Ellard, Angus Clarke, Sarah Wynn, Amanda Pichini, Celine Lewis
Whole genome sequencing (WGS) is being used in diagnostic testing for certain clinical indications within the NHS Genomic Medicine Service (GMS) in England. Letter writing is an integral part of delivering results. However, no national guidelines for writing results from WGS exist. This multi-centre service evaluation used mixed methods to understand the content and readability of letters returning diagnostic, variant of uncertain significance (VUS), and no-finding results to paediatric rare disease patients. Eight Regional Genetics Services (response rate 47%) in England provided a total of 37 letters returning diagnostic (n = 13), VUS (n = 10), and no-finding (n = 14) results. Diagnostic and VUS results were usually delivered during an appointment; no-finding results were typically delivered by letter only. Letters were diverse in which content topics they covered and level of detail. No-finding letters (14/14) explained the result but were less likely to cover other topics. Diagnostic letters discussed the result (13/13), the condition (13/13), clinical genetics follow-up (13/13), clinical management (10/13), and adapting to the result (9/13). VUS letters explained the result (10/10), diagnostic uncertainty (10/10), and clinical genetics follow-up (10/10). Uncertainty was a common component of letters (33/37), irrespective of the result. Reanalysis or review after one or more years was suggested in 6/13 diagnostic, 7/10 VUS, and 6/14 no-finding letters. The mean reading level of letters corresponded to 15–17 years. Understanding how WGS results are conveyed to families during appointments, as well as how families interpret that information, is needed to provide a more comprehensive overview of results communication and inform best practices.
{"title":"Written communication of whole genome sequencing results in the NHS Genomic Medicine Service: a multi-centre service evaluation","authors":"Holly Ellard, Angus Clarke, Sarah Wynn, Amanda Pichini, Celine Lewis","doi":"10.1038/s41431-024-01636-5","DOIUrl":"10.1038/s41431-024-01636-5","url":null,"abstract":"Whole genome sequencing (WGS) is being used in diagnostic testing for certain clinical indications within the NHS Genomic Medicine Service (GMS) in England. Letter writing is an integral part of delivering results. However, no national guidelines for writing results from WGS exist. This multi-centre service evaluation used mixed methods to understand the content and readability of letters returning diagnostic, variant of uncertain significance (VUS), and no-finding results to paediatric rare disease patients. Eight Regional Genetics Services (response rate 47%) in England provided a total of 37 letters returning diagnostic (n = 13), VUS (n = 10), and no-finding (n = 14) results. Diagnostic and VUS results were usually delivered during an appointment; no-finding results were typically delivered by letter only. Letters were diverse in which content topics they covered and level of detail. No-finding letters (14/14) explained the result but were less likely to cover other topics. Diagnostic letters discussed the result (13/13), the condition (13/13), clinical genetics follow-up (13/13), clinical management (10/13), and adapting to the result (9/13). VUS letters explained the result (10/10), diagnostic uncertainty (10/10), and clinical genetics follow-up (10/10). Uncertainty was a common component of letters (33/37), irrespective of the result. Reanalysis or review after one or more years was suggested in 6/13 diagnostic, 7/10 VUS, and 6/14 no-finding letters. The mean reading level of letters corresponded to 15–17 years. Understanding how WGS results are conveyed to families during appointments, as well as how families interpret that information, is needed to provide a more comprehensive overview of results communication and inform best practices.","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":"32 11","pages":"1436-1445"},"PeriodicalIF":3.7,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41431-024-01636-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141161487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-28DOI: 10.1038/s41431-024-01631-w
Vincent Milon, Marie-Claire Malinge, Maud Blanluet, Marine Tessarech, Clarisse Battault, Sarah Prestwich, Béatrice Vary, Pierre Gueracher, Louis Legoff, Magalie Barth, Clara Houdayer, Agnès Guichet, Audrey Rousseau, Dominique Bonneau, Vincent Procaccio, Céline Bris, Estelle Colin
Tuberous sclerosis complex (TSC) is a rare multisystemic disorder caused by a pathogenic variant in the TSC1 or TSC2 gene. A great phenotypic variability characterises TSC. The condition predisposes to the formation of hamartomas in various tissues, neurologic and neurodevelopmental disorders such as epilepsy, psychiatric disorders, as well as intellectual disability in 50%. TSC may be responsible for cardiac rhabdomyomas (CRs), cortical tubers, or subependymal nodules during foetal life. Detecting multiple CRs is associated with a very high risk of TSC, but the CR could be single and isolated. Few data exist to estimate the risk of TSC in these cases. We report the largest series of prenatal genetic tests for TSC with a retrospective study of 240 foetuses presenting with suggestive antenatal signs. We also provide a review of the literature to specify the probability of clinical or genetic diagnosis of TSC in case of detection of single or multiple CRs. Indeed, an early diagnosis is crucial for the counselling of the couple and their families. In this series, a definite diagnosis was assessed in 50% (41/82) of foetuses who initially presented with a single CR and 80.3% (127/158) in cases of multiple CRs. The prevalence of parental germinal mosaicism was 2.6% (3/115).
{"title":"Diagnosis of tuberous sclerosis in the prenatal period: a retrospective study of 240 cases and review of the literature.","authors":"Vincent Milon, Marie-Claire Malinge, Maud Blanluet, Marine Tessarech, Clarisse Battault, Sarah Prestwich, Béatrice Vary, Pierre Gueracher, Louis Legoff, Magalie Barth, Clara Houdayer, Agnès Guichet, Audrey Rousseau, Dominique Bonneau, Vincent Procaccio, Céline Bris, Estelle Colin","doi":"10.1038/s41431-024-01631-w","DOIUrl":"10.1038/s41431-024-01631-w","url":null,"abstract":"<p><p>Tuberous sclerosis complex (TSC) is a rare multisystemic disorder caused by a pathogenic variant in the TSC1 or TSC2 gene. A great phenotypic variability characterises TSC. The condition predisposes to the formation of hamartomas in various tissues, neurologic and neurodevelopmental disorders such as epilepsy, psychiatric disorders, as well as intellectual disability in 50%. TSC may be responsible for cardiac rhabdomyomas (CRs), cortical tubers, or subependymal nodules during foetal life. Detecting multiple CRs is associated with a very high risk of TSC, but the CR could be single and isolated. Few data exist to estimate the risk of TSC in these cases. We report the largest series of prenatal genetic tests for TSC with a retrospective study of 240 foetuses presenting with suggestive antenatal signs. We also provide a review of the literature to specify the probability of clinical or genetic diagnosis of TSC in case of detection of single or multiple CRs. Indeed, an early diagnosis is crucial for the counselling of the couple and their families. In this series, a definite diagnosis was assessed in 50% (41/82) of foetuses who initially presented with a single CR and 80.3% (127/158) in cases of multiple CRs. The prevalence of parental germinal mosaicism was 2.6% (3/115).</p>","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141161375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-27DOI: 10.1038/s41431-024-01628-5
Huairen Zhang, Avgi Andreou, Rupesh Bhatt, James Whitworth, Bryndis Yngvadottir, Eamonn R. Maher
In a subset of patients with renal tumours, multiple primary lesions may occur. Predisposition to multiple primary renal tumours (MPRT) is a well-recognised feature of some inherited renal cancer syndromes. The diagnosis of MPRT should therefore provoke a thorough assessment for clinical and genetic evidence of disorders associated with predisposition to renal tumourigenesis. To better define the clinical and genetic characteristics of MPRT, a systematic literature review was performed for publications up to 3 April 2024. A total of 7689 patients from 467 articles were identified with MPRT. Compared to all patients with renal cell carcinoma (RCC), patients with MPRT were more likely to be male (71.8% versus 63%) and have an earlier age at diagnosis (<46 years, 32.4% versus 19%). In 61.1% of cases MPRT were synchronous. The proportion of cases with similar histology and the proportion of cases with multiple papillary renal cell carcinoma (RCC) (16.1%) were higher than expected. In total, 14.9% of patients with MPRT had a family history of cancer or were diagnosed with a hereditary RCC associated syndrome with von Hippel-Lindau (VHL) disease being the most common one (69.7%), followed by Birt-Hogg-Dubé (BHD) syndrome (14.2%). Individuals with a known or likely genetic cause were, on average, younger (43.9 years versus 57.1 years). In rare cases intrarenal metastatic RCC can phenocopy MPRT. We review potential genetic causes of MPRT and their implications for management, suggest an approach to genetic testing for individuals presenting with MPRT and considerations in cases in which routine germline genetic testing does not provide a diagnosis.
{"title":"Characteristics, aetiology and implications for management of multiple primary renal tumours: a systematic review","authors":"Huairen Zhang, Avgi Andreou, Rupesh Bhatt, James Whitworth, Bryndis Yngvadottir, Eamonn R. Maher","doi":"10.1038/s41431-024-01628-5","DOIUrl":"10.1038/s41431-024-01628-5","url":null,"abstract":"In a subset of patients with renal tumours, multiple primary lesions may occur. Predisposition to multiple primary renal tumours (MPRT) is a well-recognised feature of some inherited renal cancer syndromes. The diagnosis of MPRT should therefore provoke a thorough assessment for clinical and genetic evidence of disorders associated with predisposition to renal tumourigenesis. To better define the clinical and genetic characteristics of MPRT, a systematic literature review was performed for publications up to 3 April 2024. A total of 7689 patients from 467 articles were identified with MPRT. Compared to all patients with renal cell carcinoma (RCC), patients with MPRT were more likely to be male (71.8% versus 63%) and have an earlier age at diagnosis (<46 years, 32.4% versus 19%). In 61.1% of cases MPRT were synchronous. The proportion of cases with similar histology and the proportion of cases with multiple papillary renal cell carcinoma (RCC) (16.1%) were higher than expected. In total, 14.9% of patients with MPRT had a family history of cancer or were diagnosed with a hereditary RCC associated syndrome with von Hippel-Lindau (VHL) disease being the most common one (69.7%), followed by Birt-Hogg-Dubé (BHD) syndrome (14.2%). Individuals with a known or likely genetic cause were, on average, younger (43.9 years versus 57.1 years). In rare cases intrarenal metastatic RCC can phenocopy MPRT. We review potential genetic causes of MPRT and their implications for management, suggest an approach to genetic testing for individuals presenting with MPRT and considerations in cases in which routine germline genetic testing does not provide a diagnosis.","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":"32 8","pages":"887-894"},"PeriodicalIF":3.7,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11291654/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141157874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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