杂合子功能缺失 SMC3 变异与不同的生长和发育特征有关。

IF 3.3 Q2 GENETICS & HEREDITY
HGG Advances Pub Date : 2024-04-11 Epub Date: 2024-01-30 DOI:10.1016/j.xhgg.2024.100273
Morad Ansari, Kamli N W Faour, Akiko Shimamura, Graeme Grimes, Emeline M Kao, Erica R Denhoff, Ana Blatnik, Daniel Ben-Isvy, Lily Wang, Benjamin M Helm, Helen Firth, Amy M Breman, Emilia K Bijlsma, Aiko Iwata-Otsubo, Thomy J L de Ravel, Vincent Fusaro, Alan Fryer, Keith Nykamp, Lara G Stühn, Tobias B Haack, G Christoph Korenke, Panayiotis Constantinou, Kinga M Bujakowska, Karen J Low, Emily Place, Jennifer Humberson, Melanie P Napier, Jessica Hoffman, Jane Juusola, Matthew A Deardorff, Wanqing Shao, Shira Rockowitz, Ian Krantz, Maninder Kaur, Sarah Raible, Victoria Dortenzio, Sabine Kliesch, Moriel Singer-Berk, Emily Groopman, Stephanie DiTroia, Sonia Ballal, Siddharth Srivastava, Kathrin Rothfelder, Saskia Biskup, Jessica Rzasa, Jennifer Kerkhof, Haley McConkey, Bekim Sadikovic, Sarah Hilton, Siddharth Banka, Frank Tüttelmann, Donald F Conrad, Anne O'Donnell-Luria, Michael E Talkowski, David R FitzPatrick, Philip M Boone
{"title":"杂合子功能缺失 SMC3 变异与不同的生长和发育特征有关。","authors":"Morad Ansari, Kamli N W Faour, Akiko Shimamura, Graeme Grimes, Emeline M Kao, Erica R Denhoff, Ana Blatnik, Daniel Ben-Isvy, Lily Wang, Benjamin M Helm, Helen Firth, Amy M Breman, Emilia K Bijlsma, Aiko Iwata-Otsubo, Thomy J L de Ravel, Vincent Fusaro, Alan Fryer, Keith Nykamp, Lara G Stühn, Tobias B Haack, G Christoph Korenke, Panayiotis Constantinou, Kinga M Bujakowska, Karen J Low, Emily Place, Jennifer Humberson, Melanie P Napier, Jessica Hoffman, Jane Juusola, Matthew A Deardorff, Wanqing Shao, Shira Rockowitz, Ian Krantz, Maninder Kaur, Sarah Raible, Victoria Dortenzio, Sabine Kliesch, Moriel Singer-Berk, Emily Groopman, Stephanie DiTroia, Sonia Ballal, Siddharth Srivastava, Kathrin Rothfelder, Saskia Biskup, Jessica Rzasa, Jennifer Kerkhof, Haley McConkey, Bekim Sadikovic, Sarah Hilton, Siddharth Banka, Frank Tüttelmann, Donald F Conrad, Anne O'Donnell-Luria, Michael E Talkowski, David R FitzPatrick, Philip M Boone","doi":"10.1016/j.xhgg.2024.100273","DOIUrl":null,"url":null,"abstract":"<p><p>Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":null,"pages":null},"PeriodicalIF":3.3000,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10876629/pdf/","citationCount":"0","resultStr":"{\"title\":\"Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features.\",\"authors\":\"Morad Ansari, Kamli N W Faour, Akiko Shimamura, Graeme Grimes, Emeline M Kao, Erica R Denhoff, Ana Blatnik, Daniel Ben-Isvy, Lily Wang, Benjamin M Helm, Helen Firth, Amy M Breman, Emilia K Bijlsma, Aiko Iwata-Otsubo, Thomy J L de Ravel, Vincent Fusaro, Alan Fryer, Keith Nykamp, Lara G Stühn, Tobias B Haack, G Christoph Korenke, Panayiotis Constantinou, Kinga M Bujakowska, Karen J Low, Emily Place, Jennifer Humberson, Melanie P Napier, Jessica Hoffman, Jane Juusola, Matthew A Deardorff, Wanqing Shao, Shira Rockowitz, Ian Krantz, Maninder Kaur, Sarah Raible, Victoria Dortenzio, Sabine Kliesch, Moriel Singer-Berk, Emily Groopman, Stephanie DiTroia, Sonia Ballal, Siddharth Srivastava, Kathrin Rothfelder, Saskia Biskup, Jessica Rzasa, Jennifer Kerkhof, Haley McConkey, Bekim Sadikovic, Sarah Hilton, Siddharth Banka, Frank Tüttelmann, Donald F Conrad, Anne O'Donnell-Luria, Michael E Talkowski, David R FitzPatrick, Philip M Boone\",\"doi\":\"10.1016/j.xhgg.2024.100273\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.</p>\",\"PeriodicalId\":34530,\"journal\":{\"name\":\"HGG Advances\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.3000,\"publicationDate\":\"2024-04-11\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10876629/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"HGG Advances\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1016/j.xhgg.2024.100273\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/1/30 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q2\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"HGG Advances","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1016/j.xhgg.2024.100273","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/30 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0

摘要

SMC3 中的杂合子错义变异和框架内缺失是科尼莉亚-德-兰格综合征(CdLS)的病因之一,该综合征以智力障碍、生长缺陷和畸形为特征,通过明显的显性阴性机制发病。然而,与 SMC3 功能缺失变异相关的表现谱尚未见报道,这导致了替代表型甚至发育致死的假设。我们利用匹配服务器、患者登记册和其他资源,确定了 SMC3 中具有杂合性、预测功能缺失(pLoF)变异的个体,并分析了人群数据库,以确定该基因突变不耐受性的特征。在这里,我们发现 SMC3 是一个典型的单倍体不足基因:它对 pLoF 变异的限制很高,对错义变异的限制很强,而且 pLoF 变异与一系列发育表型有关。在 14 个患有 SMC3 pLoF 变异的个体中,表型各不相同,但都有低生长参数、发育迟缓/智力障碍和畸形,让人联想到非典型 CdLS。与 SMC3 错义/帧内嵌合变异的个体相比,pLoF 携带者的总体表现较轻。此外,一些携带 SMC3 pLoF 变体的个体在生长、发育和/或畸形特征方面无特异性,还有一些个体的症状与 SMC3 有合理的生物学联系。对部分病例的肿瘤和模型系统转录组数据以及表观遗传学数据的分析表明,SMC3 pLoF 变异会降低 SMC3 的表达,但并不强烈支持与典型 CdLS 的功能基因组特征进行聚类。我们发现,在 SMC3 pLoF 变体的受试者中,存在大量人群规模的 LoF 不耐受现象,同时还存在不同的生长和发育特征,这一发现扩大了粘连蛋白病的范围,为其等位基因结构提供了信息,并表明还存在其他明显受 LoF 限制的基因,只有通过多层次的基因组数据和仔细的表型分析才能证实这些基因与疾病的联系。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features.

Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
HGG Advances
HGG Advances Biochemistry, Genetics and Molecular Biology-Molecular Medicine
CiteScore
4.30
自引率
4.50%
发文量
69
审稿时长
14 weeks
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信