ClinVar Genomic variation as it relates to human health
NM_007126.5(VCP):c.476G>A (p.Arg159His)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_007126.5(VCP):c.476G>A (p.Arg159His)
Variation ID: 8474 Accession: VCV000008474.48
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 9p13.3 9: 35065351 (GRCh38) [ NCBI UCSC ] 9: 35065348 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Sep 17, 2016 Oct 20, 2024 Sep 22, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_007126.5:c.476G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_009057.1:p.Arg159His missense NM_001354927.2:c.341G>A NP_001341856.1:p.Arg114His missense NM_001354928.2:c.341G>A NP_001341857.1:p.Arg114His missense NC_000009.12:g.35065351C>T NC_000009.11:g.35065348C>T NG_007887.1:g.12392G>A LRG_657:g.12392G>A LRG_657t1:c.476G>A P55072:p.Arg159His - Protein change
- R159H, R114H
- Other names
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- Canonical SPDI
- NC_000009.12:35065350:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00000
The Genome Aggregation Database (gnomAD), exomes 0.00001
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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VCP | - | - |
GRCh38 GRCh37 |
614 | 700 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (2) |
criteria provided, single submitter
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Sep 22, 2024 | RCV000008995.6 | |
Pathogenic (7) |
criteria provided, multiple submitters, no conflicts
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Jun 1, 2024 | RCV000276565.36 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 25, 2024 | RCV000639653.9 | |
VCP-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Apr 4, 2024 | RCV004532314.2 |
Pathogenic (1) |
criteria provided, single submitter
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Jan 23, 2023 | RCV003335021.4 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Jun 08, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000709188.2
First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016 |
Number of individuals with the variant: 2
Sex: mixed
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Pathogenic
(Oct 22, 2018)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000329984.5
First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016 |
Comment:
The R159H variant in the VCP gene has been reported previously in association with inclusion body myopathy, Paget disease of the bone, and frontotemporal dementia … (more)
The R159H variant in the VCP gene has been reported previously in association with inclusion body myopathy, Paget disease of the bone, and frontotemporal dementia (IBMPFD), as well as both sporadic and familial forms of amyotrophic lateral sclerosis (Haubenberger et al., 2005; Ayaki et al., 2014; van der Zee et al., 2009). In vitro expression studies of the R159H variant in SH-SY5Y cells showed a statistically significant increase in the percentage of cells with cytoplasmic TDP-43; translocation of TDP-43 to the cytoplasm and aggregation in the cytoplasm has previously been reported as a feature of VCP-related ALS (Ayaki et al., 2014). The R159H variant is observed in 1/22300 alleles from individuals of Finnish background in large population cohorts (Lek et al., 2016). Although the R159H variant is a conservative amino acid substitution, it occurs in the four-stranded b barrel in the CDC48 domain, a critical functional domain (Hubbers et al., 2007). We interpret R159H as a pathogenic variant. (less)
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Pathogenic
(Jan 23, 2023)
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criteria provided, single submitter
Method: clinical testing
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Frontotemporal dementia and/or amyotrophic lateral sclerosis 6
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
Accession: SCV004045882.1
First in ClinVar: Oct 21, 2023 Last updated: Oct 21, 2023 |
Number of individuals with the variant: 1
Clinical Features:
Muscle weakness (present) , Muscular atrophy (present) , Spasticity (present) , Elevated circulating creatine kinase concentration (present)
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Pathogenic
(Apr 28, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002020857.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Jan 25, 2024)
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criteria provided, single submitter
Method: clinical testing
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Inclusion body myopathy with Paget disease of bone and frontotemporal dementia
Frontotemporal dementia and/or amyotrophic lateral sclerosis 6
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000761233.7
First in ClinVar: May 28, 2018 Last updated: Feb 28, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 159 of the VCP protein (p.Arg159His). … (more)
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 159 of the VCP protein (p.Arg159His). This variant is present in population databases (rs121909335, gnomAD 0.004%). This missense change has been observed in individuals with inclusion body myopathy associated with Paget disease of the bone and frontotemporal dementia (IBMPFD) (PMID: 16247064, 19225410, 19704082, 22078486, 24829604, 26555887). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 8474). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt VCP protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects VCP function (PMID: 22270372, 25492614, 26555887, 27226613). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Sep 22, 2024)
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criteria provided, single submitter
Method: clinical testing
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Inclusion body myopathy with Paget disease of bone and frontotemporal dementia type 1
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV005373810.1
First in ClinVar: Oct 13, 2024 Last updated: Oct 13, 2024 |
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Pathogenic
(Jun 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001248047.26
First in ClinVar: May 09, 2020 Last updated: Oct 20, 2024 |
Comment:
VCP: PM2, PM5, PS4:Moderate, PP1, PP2, PP3, PS3:Supporting
Number of individuals with the variant: 3
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Pathogenic
(Oct 26, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Athena Diagnostics
Accession: SCV004229423.1
First in ClinVar: Jan 26, 2024 Last updated: Jan 26, 2024 |
Comment:
The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). It is statistically more frequent in affected individuals than in the … (more)
The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). It is statistically more frequent in affected individuals than in the general population and/or healthy controls. This variant has been identified in multiple unrelated individuals with clinical features of FTD/ALS as well as IBMPFD. Assessment of experimental evidence suggests this variant results in abnormal protein function. (PMIDs: 22270372, 27226613, 25492614) The variant is located in a region that is considered important for protein function and/or structure. (less)
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Pathogenic
(Aug 25, 2009)
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no assertion criteria provided
Method: literature only
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INCLUSION BODY MYOPATHY WITH EARLY-ONSET PAGET DISEASE AND FRONTOTEMPORAL DEMENTIA 1
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000029209.3
First in ClinVar: Apr 04, 2013 Last updated: Dec 26, 2020 |
Comment on evidence:
In 4 affected sibs of an Austrian family with autosomal dominant inclusion body myopathy and Paget disease but without dementia (IBMPFD1; 167320), Haubenberger et al. … (more)
In 4 affected sibs of an Austrian family with autosomal dominant inclusion body myopathy and Paget disease but without dementia (IBMPFD1; 167320), Haubenberger et al. (2005) identified a heterozygous 688G-A transition in exon 5 of the VCP gene, resulting in an arg159-to-his (R159H) substitution. The mutation occurred in a highly conserved region close to the codon 155 hotspot described by Watts et al. (2004) and was not present in 384 control chromosomes. None of the 4 affected sibs demonstrated frontotemporal dementia even though all were over 60 years of age. Haubenberger et al. (2005) noted that only approximately 30% of patients with VCP mutations develop dementia, illustrating phenotypic variability. In a follow-up of this family, van der Zee et al. (2009) noted that 1 patient had developed dementia at age 64. Van der Zee et al. (2009) also identified the R159H mutation in affected members of 2 unrelated Belgian families. In 1 family, patients presented with frontotemporal lobar degeneration only, whereas in the other family, patients developed frontotemporal lobar degeneration, Paget disease of the bone, or both without signs of inclusion body myopathy for any of the mutation carriers. Haplotype analysis showed that the 2 families and the Austrian family reported by Haubenberger et al. (2005) were unrelated. Autopsy data of 3 patients from the 2 Belgian families showed frontotemporal lobar degeneration with numerous ubiquitin-immunoreactive, intranuclear inclusions and dystrophic neurites staining positive for TDP43 (TARDBP; 605078) protein. Van der Zee et al. (2009) commented on the high degree of clinical heterogeneity and incomplete penetrance of the disorder in different families carrying the same mutation. De Ridder et al. (2020) reported a 36-year-old Belgian man with onset of IBMPFD1 at age 29 years who carried a homozygous R159H mutation in the VCP gene. His 63-year-old father, who carried the mutation in heterozygous state, had a similar myopathic phenotype with later onset at age 58. His 60-year-old mother, who was also heterozygous for the mutation, was clinically unaffected. The proband presented with progressive proximal muscle weakness with possible neurogenic features and high serum creatine kinase; an asymptomatic Paget bone lesion was later identified. Neither patient had dementia. Functional studies of the variant were not performed, but proteomic analysis of skeletal muscle from the proband and his father, as well as from 3 additional patients with VCP-related myopathy, showed changes in upstream regulators involved in myogenesis, muscle regeneration, oxidative stress, endoplasmic reticulum stress, stress granules, and the unfolded protein response. (less)
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Likely pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001926641.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
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Pathogenic
(Apr 04, 2024)
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no assertion criteria provided
Method: clinical testing
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VCP-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004744740.2
First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024 |
Comment:
The VCP c.476G>A variant is predicted to result in the amino acid substitution p.Arg159His. This variant is reported to be causative for progressive proximal myopathy … (more)
The VCP c.476G>A variant is predicted to result in the amino acid substitution p.Arg159His. This variant is reported to be causative for progressive proximal myopathy and Paget disease of the bone in four affected members of an Australian family (Haubenberger et al. 2005. PubMed ID: 16247064). It was also reported to be causative for inclusion body myopathy with early-onset Paget disease and frontotemporal dementia (IBMPFD) (van der Zee et al. 2009. PubMed ID: 19704082). In vitro functional studies in HEK293T and SH-SY5Y cells have demonstrated that expression of this variant results in TDP-43 mislocalization (Figure 6, Ayaki et al. 2014. PubMed ID: 25492614). The c.476G>A variant has also been interpreted as pathogenic in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/8474/). This variant is reported in 0.0046% of alleles in individuals of European (Finnish) descent in gnomAD. This variant is interpreted as pathogenic. (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001954556.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Genotyping and Plasma/Cerebrospinal Fluid Profiling of a Cohort of Frontotemporal Dementia-Amyotrophic Lateral Sclerosis Patients. | Bourbouli M | Brain sciences | 2021 | PMID: 34573259 |
Sequential targeted exome sequencing of 1001 patients affected by unexplained limb-girdle weakness. | Töpf A | Genetics in medicine : official journal of the American College of Medical Genetics | 2020 | PMID: 32528171 |
Screening of dementia genes by whole-exome sequencing in Spanish patients with early-onset dementia: likely pathogenic, uncertain significance and risk variants. | Ramos-Campoy O | Neurobiology of aging | 2020 | PMID: 32317127 |
A multistage sequencing strategy pinpoints novel candidate alleles for Emery-Dreifuss muscular dystrophy and supports gene misregulation as its pathomechanism. | Meinke P | EBioMedicine | 2020 | PMID: 31862442 |
Multisystem proteinopathy due to a homozygous p.Arg159His VCP mutation: A tale of the unexpected. | De Ridder W | Neurology | 2020 | PMID: 31848255 |
Predictors for a dementia gene mutation based on gene-panel next-generation sequencing of a large dementia referral series. | Koriath C | Molecular psychiatry | 2020 | PMID: 30279455 |
The multifaceted clinical presentation of VCP-proteinopathy in a Greek family. | Papadimas GK | Acta myologica : myopathies and cardiomyopathies : official journal of the Mediterranean Society of Myology | 2017 | PMID: 29770363 |
Identifying pathogenicity of human variants via paralog-based yeast complementation. | Yang F | PLoS genetics | 2017 | PMID: 28542158 |
Pathogenic Mutations in the Valosin-containing Protein/p97(VCP) N-domain Inhibit the SUMOylation of VCP and Lead to Impaired Stress Response. | Wang T | The Journal of biological chemistry | 2016 | PMID: 27226613 |
Investigating the role of filamin C in Belgian patients with frontotemporal dementia linked to GRN deficiency in FTLD-TDP brains. | Janssens J | Acta neuropathologica communications | 2015 | PMID: 26555887 |
Immunoreactivity of valosin-containing protein in sporadic amyotrophic lateral sclerosis and in a case of its novel mutant. | Ayaki T | Acta neuropathologica communications | 2014 | PMID: 25492614 |
Involvement of peripheral and central nervous systems in a valosin-containing protein mutation. | Segers K | Journal of clinical neurology (Seoul, Korea) | 2014 | PMID: 24829604 |
The role of the N-domain in the ATPase activity of the mammalian AAA ATPase p97/VCP. | Niwa H | The Journal of biological chemistry | 2012 | PMID: 22270372 |
VCP mutations in familial and sporadic amyotrophic lateral sclerosis. | Koppers M | Neurobiology of aging | 2012 | PMID: 22078486 |
Clinical heterogeneity in 3 unrelated families linked to VCP p.Arg159His. | van der Zee J | Neurology | 2009 | PMID: 19704082 |
TAR DNA-Binding protein 43 accumulation in protein aggregate myopathies. | Olivé M | Journal of neuropathology and experimental neurology | 2009 | PMID: 19225410 |
Inclusion body myopathy and Paget disease is linked to a novel mutation in the VCP gene. | Haubenberger D | Neurology | 2005 | PMID: 16247064 |
Inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia is caused by mutant valosin-containing protein. | Watts GD | Nature genetics | 2004 | PMID: 15034582 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=VCP | - | - | - | - |
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Text-mined citations for rs121909335 ...
HelpRecord last updated Nov 10, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.