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估计有多少无义变异体经历了新描述的制造剪接拯救现象。

Estimating the proportion of nonsense variants undergoing the newly described phenomenon of manufactured splice rescue.

机构信息

Program in Genetics & Genome Biology, SickKids Research Institute, Toronto, ON, Canada.

Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.

出版信息

Eur J Hum Genet. 2024 Feb;32(2):238-242. doi: 10.1038/s41431-023-01495-6. Epub 2023 Nov 27.


DOI:10.1038/s41431-023-01495-6
PMID:38012313
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10853237/
Abstract

A recent report described a nonsense variant simultaneously creating a donor splice site, resulting in a truncated but functional protein. To explore the generalizability of this unique mechanism, we annotated >115,000 nonsense variants using SpliceAI. Between 0.61% (donor gain delta score >0.8, for high precision) and 2.57% (>0.2, for high sensitivity) of nonsense variants were predicted to create new donor splice sites at or upstream of the stop codon. These variants were less likely than other nonsense variants in the same genes to be classified as pathogenic/likely pathogenic in ClinVar (p < 0.001). Up to 1 in 175 nonsense variants were predicted to result in small in-frame deletions and loss-of-function evasion through this "manufactured splice rescue" mechanism. We urge caution when interpreting nonsense variants where manufactured splice rescue is a strong possibility and correlation with phenotype is challenging, as will often be the case with secondary findings and newborn genomic screening programs.

摘要

最近的一份报告描述了一种无意义变异同时创建供体位点,导致截短但功能完整的蛋白质。为了探索这种独特机制的普遍性,我们使用 SpliceAI 注释了 >115,000 个无意义变异。在 0.61%(供体位点增益分数>0.8,高精度)和 2.57%(>0.2,高灵敏度)的无意义变异被预测在终止密码子或其上游创建新的供体位点。与同一基因中其他无意义变异相比,这些变异在 ClinVar 中被归类为致病性/可能致病性的可能性更小(p<0.001)。多达 1/175 个无意义变异被预测会导致小的框内缺失,并通过这种“制造的剪接拯救”机制逃避功能丧失。当制造的剪接拯救可能性很大且与表型相关具有挑战性时,我们应谨慎解释无意义变异,这种情况在二级发现和新生儿基因组筛查计划中经常出现。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ca9f/10853237/252530daad02/41431_2023_1495_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ca9f/10853237/1effb538a8c3/41431_2023_1495_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ca9f/10853237/c8c58fcba8b0/41431_2023_1495_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ca9f/10853237/252530daad02/41431_2023_1495_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ca9f/10853237/1effb538a8c3/41431_2023_1495_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ca9f/10853237/c8c58fcba8b0/41431_2023_1495_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ca9f/10853237/252530daad02/41431_2023_1495_Fig3_HTML.jpg

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[1]
Estimating the proportion of nonsense variants undergoing the newly described phenomenon of manufactured splice rescue.

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引用本文的文献

[1]
Assessing Splicing Variants in the PAX6 Gene: A Comprehensive Minigene Approach.

J Cell Mol Med. 2025-3

[2]
Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data.

Nat Commun. 2025-1-9

[3]
International policies guiding the selection, analysis, and clinical management of secondary findings from genomic sequencing: A systematic review.

Am J Hum Genet. 2024-10-3

[4]
Loss-of-function variants affecting the STAGA complex component SUPT7L cause a developmental disorder with generalized lipodystrophy.

Hum Genet. 2024-5

[5]
Using exomes better.

Eur J Hum Genet. 2024-2

本文引用的文献

[1]
Advanced variant classification framework reduces the false positive rate of predicted loss-of-function variants in population sequencing data.

Am J Hum Genet. 2023-9-7

[2]
Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup.

Am J Hum Genet. 2023-7-6

[3]
Trio RNA sequencing in a cohort of medically complex children.

Am J Hum Genet. 2023-5-4

[4]
Genomic architecture of autism from comprehensive whole-genome sequence annotation.

Cell. 2022-11-10

[5]
InterPro in 2022.

Nucleic Acids Res. 2023-1-6

[6]
A novel nonsense variant in ARID1B causing simultaneous RNA decay and exon skipping is associated with Coffin-Siris syndrome.

Hum Genome Var. 2022-7-25

[7]
Recommendations for clinical interpretation of variants found in non-coding regions of the genome.

Genome Med. 2022-7-19

[8]
Alternative splicing of BUD13 determines the severity of a developmental disorder with lipodystrophy and progeroid features.

Genet Med. 2022-9

[9]
Genome sequencing for detection of pathogenic deep intronic variation: A clinical case report illustrating opportunities and challenges.

Am J Med Genet A. 2021-10

[10]
The mutational constraint spectrum quantified from variation in 141,456 humans.

Nature. 2020-5-27

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