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NM_007126.5(VCP):c.463C>G (p.Arg155Gly) AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 9, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002229498.13

Allele description [Variation Report for NM_007126.5(VCP):c.463C>G (p.Arg155Gly)]

NM_007126.5(VCP):c.463C>G (p.Arg155Gly)

Gene:
VCP:valosin containing protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9p13.3
Genomic location:
Preferred name:
NM_007126.5(VCP):c.463C>G (p.Arg155Gly)
HGVS:
  • NC_000009.12:g.35065364G>C
  • NG_007887.1:g.12379C>G
  • NM_001354927.2:c.328C>G
  • NM_001354928.2:c.328C>G
  • NM_007126.5:c.463C>GMANE SELECT
  • NP_001341856.1:p.Arg110Gly
  • NP_001341857.1:p.Arg110Gly
  • NP_009057.1:p.Arg155Gly
  • LRG_657t1:c.463C>G
  • LRG_657:g.12379C>G
  • NC_000009.11:g.35065361G>C
  • NM_007126.3:c.463C>G
Protein change:
R110G
Links:
dbSNP: rs121909330
NCBI 1000 Genomes Browser:
rs121909330
Molecular consequence:
  • NM_001354927.2:c.328C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354928.2:c.328C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007126.5:c.463C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Frontotemporal dementia and/or amyotrophic lateral sclerosis 6 (FTDALS6)
Synonyms:
Amyotrophic lateral sclerosis 14, with or without frontotemporal dementia; VCP-Related Amyotrophic Lateral Sclerosis; VCP-Related Amyotrophic Lateral Sclerosis/Frontotemporal Dementia
Identifiers:
MONDO: MONDO:0013501; MedGen: C5436279; Orphanet: 275872; Orphanet: 803; OMIM: 613954
Name:
Inclusion body myopathy with Paget disease of bone and frontotemporal dementia
Synonyms:
Inclusion body myopathy with early-onset Paget disease and frontotemporal dementia
Identifiers:
MONDO: MONDO:0000507; MedGen: C1833662; OMIM: PS167320

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000940847Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Aug 9, 2022)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Clinical exome sequencing for genetic identification of rare Mendelian disorders.

Lee H, Deignan JL, Dorrani N, Strom SP, Kantarci S, Quintero-Rivera F, Das K, Toy T, Harry B, Yourshaw M, Fox M, Fogel BL, Martinez-Agosto JA, Wong DA, Chang VY, Shieh PB, Palmer CG, Dipple KM, Grody WW, Vilain E, Nelson SF.

JAMA. 2014 Nov 12;312(18):1880-7. doi: 10.1001/jama.2014.14604.

PubMed [citation]
PMID:
25326637
PMCID:
PMC4278636

Inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia is caused by mutant valosin-containing protein.

Watts GD, Wymer J, Kovach MJ, Mehta SG, Mumm S, Darvish D, Pestronk A, Whyte MP, Kimonis VE.

Nat Genet. 2004 Apr;36(4):377-81. Epub 2004 Mar 21.

PubMed [citation]
PMID:
15034582
See all PubMed Citations (7)

Details of each submission

From Invitae, SCV000940847.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

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 expected to disrupt VCP protein function. ClinVar contains an entry for this variant (Variation ID: 217028). This missense change has been observed in individual(s) with myopathy (PMID: 25326637). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 155 of the VCP protein (p.Arg155Gly). This variant disrupts the p.Arg155 amino acid residue in VCP. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 15034582, 16790606, 17763460, 19364651, 26105173). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 7, 2024