NM_020631.6(PLEKHG5):c.1379G>A (p.Arg460Gln) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Jul 25, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000556509.1

Allele description [Variation Report for NM_020631.6(PLEKHG5):c.1379G>A (p.Arg460Gln)]

NM_020631.6(PLEKHG5):c.1379G>A (p.Arg460Gln)

Gene:
PLEKHG5:pleckstrin homology and RhoGEF domain containing G5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.31
Genomic location:
Preferred name:
NM_020631.6(PLEKHG5):c.1379G>A (p.Arg460Gln)
HGVS:
  • NC_000001.11:g.6471003C>T
  • NG_007978.1:g.54007G>A
  • NG_029910.1:g.193G>A
  • NM_001042663.3:c.1490G>A
  • NM_001042664.1:c.1379G>A
  • NM_001042665.1:c.1379G>A
  • NM_001265592.2:c.1490G>A
  • NM_001265593.1:c.1586G>A
  • NM_001265594.2:c.1379G>A
  • NM_020631.6:c.1379G>AMANE SELECT
  • NM_198681.4:c.1379G>A
  • NP_001036128.2:p.Arg497Gln
  • NP_001036129.1:p.Arg460Gln
  • NP_001036130.1:p.Arg460Gln
  • NP_001252521.2:p.Arg497Gln
  • NP_001252522.1:p.Arg529Gln
  • NP_001252523.1:p.Arg460Gln
  • NP_065682.2:p.Arg460Gln
  • NP_941374.3:p.Arg460Gln
  • LRG_262:g.54007G>A
  • NC_000001.10:g.6531063C>T
  • NM_020631.4:c.1379G>A
Protein change:
R460Q
Links:
dbSNP: rs1309731055
NCBI 1000 Genomes Browser:
rs1309731055
Molecular consequence:
  • NM_001042663.3:c.1490G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042664.1:c.1379G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042665.1:c.1379G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001265592.2:c.1490G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001265593.1:c.1586G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001265594.2:c.1379G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020631.6:c.1379G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198681.4:c.1379G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Distal spinal muscular atrophy, autosomal recessive 4 (DSMA4)
Identifiers:
MONDO: MONDO:0012608; MedGen: C1970211; Orphanet: 206580; OMIM: 611067
Name:
Charcot-Marie-Tooth disease, recessive intermediate c (CMTRIC)
Synonyms:
CHARCOT-MARIE-TOOTH NEUROPATHY, RECESSIVE INTERMEDIATE C
Identifiers:
MONDO: MONDO:0014154; MedGen: C3809309; Orphanet: 369867; OMIM: 615376

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000646004Invitaecriteria provided, single submitter
Uncertain significance
(Jul 25, 2017)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000646004.1

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

Description

This sequence change replaces arginine with glutamine at codon 460 of the PLEKHG5 protein (p.Arg460Gln). The arginine residue is moderately conserved and there is a small physicochemical difference between arginine and glutamine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with PLEKHG5-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 25, 2021

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