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Human Molecular Genetics
Article . 2022 . Peer-reviewed
License: OUP Standard Publication Reuse
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DIGITAL.CSIC
Article . 2023 . Peer-reviewed
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https://doi.org/10.1101/2022.0...
Article . 2022 . Peer-reviewed
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A KLHL40 3’ UTR splice-altering variant causes milder NEM8, an under-appreciated disease mechanism

Authors: Lein N.H. Dofash; Gavin Monahan; Emilia Servián-Morilla; Eloy Rivas; Fathimath Faiz; Patricia Sullivan; Emily Oates; +7 Authors

A KLHL40 3’ UTR splice-altering variant causes milder NEM8, an under-appreciated disease mechanism

Abstract

Abstract Nemaline myopathy 8 (NEM8) is typically a severe autosomal recessive disorder associated with variants in the kelch-like family member 40 gene (KLHL40). Common features include fetal akinesia, fractures, contractures, dysphagia, respiratory failure and neonatal death. Here, we describe a 26-year-old man with relatively mild NEM8. He presented with hypotonia and bilateral femur fractures at birth, later developing bilateral Achilles’ contractures, scoliosis, and elbow and knee contractures. He had walking difficulties throughout childhood and became wheelchair bound from age 13 after prolonged immobilization. Muscle magnetic resonance imaging at age 13 indicated prominent fat replacement in his pelvic girdle, posterior compartments of thighs and vastus intermedius. Muscle biopsy revealed nemaline bodies and intranuclear rods. RNA sequencing and western blotting of patient skeletal muscle indicated significant reduction in KLHL40 mRNA and protein, respectively. Using gene panel screening, exome sequencing and RNA sequencing, we identified compound heterozygous variants in KLHL40; a truncating 10.9 kb deletion in trans with a likely pathogenic variant (c.*152G > T) in the 3′ untranslated region (UTR). Computational tools SpliceAI and Introme predicted the c.*152G > T variant created a cryptic donor splice site. RNA-seq and in vitro analyses indicated that the c.*152G > T variant induces multiple de novo splicing events that likely provoke nonsense mediated decay of KLHL40 mRNA explaining the loss of mRNA expression and protein abundance in the patient. Analysis of 3’ UTR variants in ClinVar suggests variants that introduce aberrant 3’ UTR splicing may be underrecognized in Mendelian disease. We encourage consideration of this mechanism during variant curation.

Country
Spain
Keywords

Male, Adult, Contracture, Adolescent, Infant, Newborn, Muscle Proteins, Myopathies, Nemaline, Mutation, Humans, RNA Splice Sites, RNA, Messenger, Child, 3' Untranslated Regions

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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