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表型-基因型IMNEPD病例更新及新基因变异的生物信息学分析

An Update of Phenotypic-Genotypic IMNEPD Cases and a Bioinformatics Analysis of the New Gene Variants.

作者信息

Sharkia Rajech, Vuillaume Marie-Laure, Jain Sahil, Mahajnah Muhammad, Stoeva Radka, Guichet Agnès, Colin Estelle, Champ Jérome, Derive Nicolas, Chefdor Arnaud, Zalan Abdelnaser

机构信息

Unit of Human Biology and Genetics, The Triangle Regional Research and Development Center, Kafr Qari 3007500, Israel.

Unit of Natural Sciences, Beit-Berl Academic College, Beit-Berl 4490500, Israel.

出版信息

Genes (Basel). 2024 Nov 25;15(12):1508. doi: 10.3390/genes15121508.

DOI:10.3390/genes15121508
PMID:39766776
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11675358/
Abstract

BACKGROUND/OBJECTIVES: Biallelic mutations in the gene are associated with a rare genetic disease known as infantile-onset multisystem neurologic, endocrine, and pancreatic disease (IMNEPD). In this study, we describe a new case carrying a previously identified mutation, provide an updated analysis of the relative frequencies of the clinical features across all published cases (including the three latest studies), and perform a bioinformatics analysis of the newly identified PTRH2 protein variants from a structural perspective.

METHODS

Clinical examination of the patients was carried out, and genetic testing was performed using a genome sequencing strategy. A bioinformatics analysis was carried out for the newly reported mutations using PYMOL that was utilized to view the structure and analyze the mutations. Additionally, the ThermoMPNN webserver was employed to check the effect of point mutations on the overall stability of the protein.

RESULTS

Our findings indicate that motor delay, neuropathy, intellectual disability, distal weakness, hearing impairment, and ataxia are the most common symptoms, while the other clinical features fall into two frequency categories: moderately common ones and the least common ones. The bioinformatics analysis revealed that the Q85 residue is highly conserved, suggesting that mutations at this position could disrupt key signaling pathways or cellular functions. Indeed, the Q85R mutation was shown to significantly impair the stability and functionality of the protein.

CONCLUSIONS

The clinical presentation of IMNEPD remains highly variable in terms of both severity and progression. Mutations at the Q85 residue have been identified in nearly 50% of reported cases, highlighting this position as a potential mutational hotspot in the PTRH2 protein.

摘要

背景/目的:该基因的双等位基因突变与一种罕见的遗传性疾病相关,即婴儿期起病的多系统神经、内分泌和胰腺疾病(IMNEPD)。在本研究中,我们描述了一例携带先前已鉴定突变的新病例,对所有已发表病例(包括三项最新研究)的临床特征相对频率进行了更新分析,并从结构角度对新鉴定的PTRH2蛋白变体进行了生物信息学分析。

方法

对患者进行了临床检查,并采用基因组测序策略进行了基因检测。使用PYMOL对新报道的突变进行了生物信息学分析,PYMOL用于查看结构和分析突变。此外,还使用了ThermoMPNN网络服务器来检查点突变对蛋白质整体稳定性的影响。

结果

我们的研究结果表明,运动发育迟缓、神经病变、智力障碍、远端肌无力、听力障碍和共济失调是最常见的症状,而其他临床特征分为两个频率类别:中度常见和最不常见。生物信息学分析显示,Q85残基高度保守,表明该位置的突变可能会破坏关键信号通路或细胞功能。事实上,Q85R突变被证明会显著损害蛋白质的稳定性和功能。

结论

IMNEPD的临床表现无论在严重程度还是进展方面都仍然高度可变。在近50%的报道病例中发现了Q85残基的突变,突出了该位置作为PTRH2蛋白潜在突变热点的地位。

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本文引用的文献

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Severe Respiratory and Swallowing Disorders in Infantile-Onset Multisystem Neurologic, Endocrine, and Pancreatic Disease Type 1: Two Cases.1型婴儿期起病的多系统神经、内分泌和胰腺疾病中的严重呼吸和吞咽障碍:两例报告
Neurol Genet. 2024 Aug 21;10(5):e200178. doi: 10.1212/NXG.0000000000200178. eCollection 2024 Oct.
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A Novel PTRH2 Gene Mutation Causing Infantile-onset Multisystem Neurologic, Endocrine, and Pancreatic Disease in a Bahraini Patient.一名巴林患者中导致婴儿期起病的多系统神经、内分泌和胰腺疾病的新型PTRH2基因突变
Oman Med J. 2024 Jan 31;39(1):e599. doi: 10.5001/omj.2024.08. eCollection 2024 Jan.
3
Transfer learning to leverage larger datasets for improved prediction of protein stability changes.
利用更大的数据集进行迁移学习,以提高蛋白质稳定性变化预测的准确性。
Proc Natl Acad Sci U S A. 2024 Feb 6;121(6):e2314853121. doi: 10.1073/pnas.2314853121. Epub 2024 Jan 29.
4
Gene Variants: Recent Review of the Phenotypic Features and Their Bioinformatics Analysis.基因变异:表型特征及其生物信息学分析的最新综述。
Genes (Basel). 2023 Apr 30;14(5):1031. doi: 10.3390/genes14051031.
5
Novel PTRH2 gene variant causing IMNEPD (infantile-onset multisystem neurologic, endocrine, and pancreatic disease) in 2 Saudi siblings.一种新型PTRH2基因变异导致2名沙特兄弟姐妹患IMNEPD(婴儿期起病的多系统神经、内分泌和胰腺疾病)
Clin Exp Pediatr. 2023 May;66(5):223-225. doi: 10.3345/cep.2022.01074. Epub 2023 Mar 23.
6
The first case of infantile-onset multisystem neurologic, endocrine, and pancreatic disease caused by novel PTRH2 mutation in Japan.日本首例由新型PTRH2突变引起的婴儿期发病的多系统神经、内分泌和胰腺疾病。
Neurol Sci. 2022 Mar;43(3):2133-2136. doi: 10.1007/s10072-021-05817-8. Epub 2022 Jan 14.
7
Highly accurate protein structure prediction with AlphaFold.利用 AlphaFold 进行高精度蛋白质结构预测。
Nature. 2021 Aug;596(7873):583-589. doi: 10.1038/s41586-021-03819-2. Epub 2021 Jul 15.
8
A novel PTRH2 missense mutation causing IMNEPD: a case report.一种导致IMNEPD的新型PTRH2错义突变:病例报告
Hum Genome Var. 2021 Jun 10;8(1):23. doi: 10.1038/s41439-021-00147-9.
9
A Novel Synergistic Association of Variants in PTRH2 and KIF1A Relates to a Syndrome of Hereditary Axonopathy, Outer Hair Cell Dysfunction, Intellectual Disability, Pancreatic Lipomatosis, Diabetes, Cerebellar Atrophy, and Vertebral Artery Hypoplasia.PTRH2和KIF1A基因变异的一种新型协同关联与一种遗传性轴索性神经病、外毛细胞功能障碍、智力残疾、胰腺脂肪瘤病、糖尿病、小脑萎缩和椎动脉发育不全综合征相关。
Cureus. 2021 Feb 6;13(2):e13174. doi: 10.7759/cureus.13174.
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