Cited by 2Hereditary Neurological DisordersGenetic Neurodegenerative DiseasesRNA Research and Splicing

The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index; none of the 17 sources its claims cite is checked for support yet.

Case report: A novel WASHC5 variant altering mRNA splicing causes spastic paraplegia in a patient

Open access

Abstract

Background: Hereditary spastic paraplegia (HSP) is a progressive upper-motor neurodegenerative disease. Mutations in the WASHC5 gene are associated with autosomal dominant HSP, spastic paraplegia 8 (SPG8). However, due to the small number of reported cases, the exact mechanism remains unclear. Method: We report a Chinese family with HSP. The proband was referred to our hospital due to restless leg syndrome and insomnia. The preliminary clinical diagnosis of the proband was spastic paraplegia. Whole-exome sequencing (WES) and RNA splicing analysis were conducted to evaluate the genetic cause of the disease in this family. Results: A novel splice-altering variant (c.712–2A>G) in the WASHC5 gene was detected and further verified by RNA splicing analysis and Sanger sequencing. Real-time qPCR analysis showed that the expression of genes involved in the Wiskott–Aldrich syndrome protein and SCAR homolog (WASH) complex and endosomal and lysosomal systems was altered due to this variant. Conclusion: A novel heterozygous splice-altering variant (c.712–2A>G) in the WASHC5 gene was detected in a Chinese family with HSP. Our study provided data for genetic counseling to this family and offered evidence that this splicing variant in the WASHC5 gene is significant in causing HSP.

Overview

AI snapshot

Written from the paper’s full text.

TL;DR

This case report identifies a novel heterozygous WASHC5 splice variant (c.712–2A>G) in a Chinese family with hereditary spastic paraplegia, molecularly diagnosing the proband with SPG8. RNA analysis shows the variant causes intron 6 retention and a 10-amino-acid insertion, with altered expression of WASH complex, endosomal, and lysosomal genes.

Key findings

  • A novel heterozygous WASHC5 variant, chr8:126088744T>C / NM_014846.4:c.712–2A>G, was detected in the proband and classified as “likely pathogenic” by ACMG criteria (PVS1 and PM2); it was absent from 1,000G, ExAC, and ESP6500 and had a GnomAD frequency of 0.000004 (1/251100).
  • RNA splicing analysis showed the variant produced a 337-nucleotide aberrant PCR product versus the expected 307-nucleotide wild-type product, retaining 30 nucleotides of intron 6 and inserting 10 aberrant amino acids (LSRGVVLTLR) at position 237, resulting in an abnormally prolonged protein of 1,169 aa.
  • Co-segregation analysis found the variant absent in healthy family members II-1, III-1, III-2, and IV-1; the proband was diagnosed with SPG8.
  • qPCR in peripheral blood lymphocytes showed significantly decreased WASHC1 and WASHC3 mRNA, significantly increased VCP mRNA, significantly changed ARPC3 expression, and significantly upregulated endosomal-related genes (RAB5A, RAB5C, RAB11A, RAB11B) and lysosome-related genes (LAPTM4B, LAPTM5) in the proband compared with healthy family members.

Methods

  • Case report of a Chinese family; the proband was a 58-year-old woman referred for restless legs syndrome and insomnia, with preliminary clinical diagnosis of spastic paraplegia.
  • Whole-exome sequencing yielded 10.21 GB data with 98.1% coverage of target regions and 96.0% of target covered over ×10; variants were filtered using a movement-disorders gene panel, and Sanger sequencing was performed in available family members.
  • RNA splicing analysis used peripheral blood cDNA with PCR, agarose gel electrophoresis, and Sanger sequencing; real-time qPCR measured mRNA from peripheral blood lymphocytes of the proband (II-3) and two healthy female family members (II-1 and III-2), normalized to ACTB using the 2−ΔΔCT method, with unpaired Student’s t-test and p < 0.05 considered significant.

Limitations

  • The paper states that deceased family members I-2 and II-2 were considered affected by relatives but could not be tested because DNA was unavailable, and the proband’s younger son III-3 died in a car crash at age 15 before any possible onset, so his genetic status was unknown.
  • The paper states that inadequate patient cooperation during testing prevented other diagnostic data from being obtained, and that additional functional analyses, such as whether the variant affects protein stability and half-life, are recommended; the endosomal/lysosomal involvement is described as a hypothesis that requires further study.
  • Evident from the text: this is a single-family case report with qPCR performed in only three female subjects, no independent replication or protein-level functional validation, and no direct testing of the deceased affected relatives.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.3389/fgene.2023.1205052

Cites

31 of 31 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Verification

Claims the paper makes

0 of 17 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    SWISS-MODEL predicted that the splice variant may lead to an insertion of 10 amino acids behind Q237 in the mutated WASHC5 protein.

    “SWISS-MODEL software (https://swissmodel.expasy.org/) showed that the splice variant may lead to an insertion of 10 amino acids behind Q237 in the mutated WASHC5 protein (Figure 2A).”
    Quote in the paperSubstantial claim
  • Findingnone given

    There was no evidence indicating the presence of peripheral neuropathy in the proband.

    “There was no evidence indicating the presence of peripheral neuropathy in the proband.”
    Quote in the paperNot a substantial claim
  • Findingcitation

    Under ACMG guidelines with evidence PVS1 and PM2, the c.712-2A>G variant is classified as likely pathogenic.

    “According to the American College of Medical Genetics and Genomics (ACMG) guidelines (Miller et al., 2021), with the following evidence: PVS1 and PM2, the c.712–2A>G variant is classified as “likely pathogenic.””
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Miller et al., 2021 source
  • Findingown data

    The proband showed asymmetric spasticity of a single lower extremity.

    “Notably, our proband showed asymmetric spasticity of a single lower extremity.”
    Quote in the paperSubstantial claim
  • Findingown data

    The proband had lower mRNA level of the ARPC3 gene compared with healthy family members.

    “The results showed that there was a significant change in the proband’s ARPC3 gene expression (Figure 2E).”
    • Also stated in: § Discussion · plain
      “we found that the proband with the splice variant had a higher mRNA level of the VCP gene and lower mRNA level of the ARPC3 gene.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim. 13
  • It may state two separate claims as one. 11
  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Findingnone given

    The proband was initially clinically diagnosed with spastic paraplegia.

    “The proband was initially clinically diagnosed with spastic paraplegia.”
    Quote in the paperNot a substantial claim
  • It may state two separate claims as one.

    Findingown data

    The retention of 30 nucleotides leads to insertion of 10 aberrant amino acids (LSRGVVLTLR) at position 237 of the WASHC5 protein, resulting in an abnormally prolonged protein of 1,169 amino acids.

    “The retention of 30 nucleotides leads to the insertion of 10 aberrant amino acids (LSRGVVLTLR) at position 237 of the WASHC5 protein, thus resulting in an abnormally prolonged protein (1,169 aa) (Figures 1I, K).”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Findingown data

    The self-rating anxiety scale and self-rating depression scale showed mild anxiety (SAS score 51) and severe depression (SDS score 0.75) in the proband.

    “The self-rating anxiety scale (SAS) and self-rating depression scale (SDS) (Yue et al., 2020) were carried out, and the results showed mild anxiety (SAS score: 51, range 0–100) and severe depression (SDS score: 0.75, range 0–1).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Yue et al., 2020 source
  • It may state two separate claims as one.

    Findingown data

    The c.712-2A>G variant is absent from the 1,000 Genomes Project, ExAC, and ESP6500 databases and has a frequency of 0.000004 (1/251100) in gnomAD.

    “The c.712–2A>G variant was not found in the 1,000 Genomes Project (1,000G; http://www.1000genomes.org/), the Exome Aggregation Consortium (ExAC) database (http://exac.broadinstitute.org), and the NHLBI Exome Sequencing Project Exome Variant Server (ESP6500) and has a frequency of 0.000004 (1/251100) in the Genome Aggregation Database (GnomAD; http://gnomad.broadinstitule.org).”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Findingown data

    The electroencephalogram showed mild abnormalities.

    “The electroencephalogram (EEG) showed mild abnormalities (Figure 1E).”
    Quote in the paperNot a substantial claim
  • It may state two separate claims as one.

    Findingown data

    Brain MRI of the proband showed mild brain atrophy, and spinal cord MRI scans were normal.

    “The brain magnetic resonance imaging (MRI) of the proband showed mild brain atrophy (Figure 1A). The spinal cord MRI scans were normal (Figures 1B–D).”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Findingown data

    Electromyography revealed absence of spontaneous muscle activity in the examined muscles of the proband's left lower limb.

    “The electromyography results revealed the absence of spontaneous muscle activity in the examined muscles of the proband’s left lower limb.”
    Quote in the paperNot a substantial claim
  • It may state two separate claims as one.

    Findingown data

    The proband with the heterozygous c.712-2A>G variant showed two PCR products of 307 and 337 nucleotides, corresponding to the wild-type and mutated allele, while relatives without the variant only had a single 307-nucleotide product.

    “The Sanger sequence analysis of the region encompassing exon 6 and exon 7 found that the proband with the heterozygous c.712–2A>G variant showed two PCR products of 307 nucleotides and 337 nucleotides, corresponding to the wild-type and the mutated allele, respectively.”
    • Also stated in: § RNA splicing analysis · plain
      “In contrast, relatives without the c.712–2A>G variant only had a single PCR product of the expected size (307 nucleotides) (Figure 1J).”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim. It may state two separate claims as one.

    Study design and conductnone given

    Two groups were compared using the unpaired Student's t-test, and a p-value <0.05 was considered statistically significant.

    “Two groups were compared using the unpaired Student’s t-test. A p-value <0.05 was considered statistically significant.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    SPG8 is a rare autosomal dominant HSP characterized by onset of progressive lower limb spasticity and hyperreflexia in adults, resulting in impaired gait and difficulty in walking.

    “SPG8 is a rare autosomal dominant HSP characterized by onset of progressive lower limb spasticity and hyperreflexia in adults, resulting in impaired gait and difficulty in walking.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites de Bot et al., 2013 source
  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    Strumpellin, encoded by WASHC5, is a key member of the WASH complex and can activate the ARP2/3 complex and interact with p97/VCP.

    “Strumpellin, encoded by the WASHC5 gene, is a key member of the Wiskott–Aldrich syndrome protein and SCAR homolog (WASH) complex. Strumpellin can activate the ubiquitous actin-related protein 2/3 (ARP2/3) complex and interact with p97/VCP (Fokin et al., 2021; Song et al., 2018).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Fokin et al., 2021 source
    • cites Song et al., 2018 source
  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    WASH complex-mediated actin is essential for both endosomal and lysosomal networks.

    “WASH complex-mediated actin is essential for both endosomal and lysosomal networks (Courtland et al., 2021; Gomez et al., 2012).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Courtland et al., 2021 source
    • cites Gomez et al., 2012 source
  • Probably not a substantial claim. It may state two separate claims as one.

    Premisecitation

    Pathogenic WASHC5 mutations in strumpellin can induce defects in endosomal fission or lysosome morphology, which further leads to HSP.

    “Pathogenic WASHC5 mutations in strumpellin can induce defects in endosomal fission or lysosome morphology, which further leads to HSP (Lee et al., 2020; Song et al., 2018).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Lee et al., 2020 source
    • cites Song et al., 2018 source
  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    To date, approximately 37 variants in WASHC5, including three splice mutations and one gross deletion variant, have been identified in a range of phenotypes.

    “To date, approximately 37 variants in WASHC5, including three splice mutations and one gross deletion variant, have been identified in a range of phenotypes (Elliott et al., 2013; Mulroy et al., 2021; D'Amore et al., 2018; Ma et al., 2018).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Elliott et al., 2013 source
    • cites Mulroy et al., 2021 source
    • cites D'Amore et al., 2018 source
  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Study design and conductown data

    WES yielded 10.21 GB data with 98.1% coverage of the target regions and 96.0% of the target covered over ×10.

    “WES yielded 10.21 GB data with 98.1% coverage of the target regions and 96.0% of the target covered over ×10.”
    Quote in the paperNot a substantial claim
  • It may state two separate claims as one.

    Premisecitation

    Disruption of either one of the five WASH complex subunits makes the whole complex unstable and may disturb the quantity of other WASH complex members.

    “Previous studies have reported that disruption of either one of the five WASH complex subunits makes the whole complex unstable and may disturb the quantity of other WASH complex members (Jahic et al., 2015; Song et al., 2018).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Jahic et al., 2015 source
    • cites Song et al., 2018 source
  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Abnormal strumpellin may lead to defects in the endosomal and lysosomal systems.

    “Furthermore, the abnormal strumpellin may lead to defects in the endosomal and lysosomal systems (Gomez et al., 2012; Lee et al., 2020; Song et al., 2018).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Gomez et al., 2012 source
    • cites Lee et al., 2020 source
    • cites Song et al., 2018 source
  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    The qPCR experiment was repeated more than three times.

    “The experiment was repeated more than three times.”
    Quote in the paperNot a substantial claim
18 of 18
  • The paper relies on this without support.

    Mutations in the WASHC5 gene can lead to SPG8.

    “Mutations in the WASHC5 gene, also known as the KIAA0196 gene, can lead to SPG8 (OMIM#603563).”
    “Mutations in the WASHC5 gene are associated with autosomal dominant HSP, spastic paraplegia 8 (SPG8).”
  • The authors state this as an assumption.

    The deceased family members I-2 and II-2 were affected by the disease.

    “The deceased family members (I-2 and II-2) were not examined; however, they were considered affected according to relatives.”
  • The paper relies on this without support.

    The c.712–2A>G variant has not been published.

    “Notably, the c.712–2A>G variant reported in this study has not been published; therefore, it is considered novel.”
3 of 3

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Splicing result cites the WES-filtering panel

    Minor

    The discussion cites Figure 1H for the aberrant transcript, but the figure legend identifies panel H as the WES filtering schematic, not a transcript result.

1 of 1

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Metadata

Authors
Gao, S.-Y., Liu, Y.-X., Dong, Y., Fan, L.-L., Ding, Q., & Liu, L.
Affiliations
  • Central South University (CN)
  • Changshu No. 2 People's Hospital (CN)
Corresponding author
  • Ding, Qi
  • Liu, Lv
Venue
Frontiers in Genetics
Published
2023-10-31
Volume
14
Pages
1205052-1205052
ISSN
1664-8021 (ISSN-L)
OpenAlex
W4388047460
Cited by
2
References
31
Citations by year
2026: 1 · 2025: 1
FWCI
0.20
Type
journal article
Language
en
Open access
Locations
  • Frontiers in Genetics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
National Natural Science Foundation of China (82000079)
Topics
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Hereditary Neurological Disorders
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Genetic Neurodegenerative Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords
hereditary spastic paraplegia, splice-altering variants, mRNA splicing, WASH complex, Wiskott-Aldrich syndrome protein, restless legs syndrome, autosomal dominant inheritance, genetic counseling

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