NM_020631.6(PLEKHG5):c.2867G>A (p.Arg956Lys) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Jun 20, 2017)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000724525.2

Allele description [Variation Report for NM_020631.6(PLEKHG5):c.2867G>A (p.Arg956Lys)]

NM_020631.6(PLEKHG5):c.2867G>A (p.Arg956Lys)

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.2867G>A (p.Arg956Lys)
HGVS:
  • NC_000001.11:g.6467969C>T
  • NG_007978.1:g.57041G>A
  • NG_029910.1:g.3227G>A
  • NM_001042663.3:c.2978G>A
  • NM_001042664.1:c.2867G>A
  • NM_001042665.1:c.2867G>A
  • NM_001265592.2:c.2978G>A
  • NM_001265593.1:c.3074G>A
  • NM_001265594.2:c.2738-71G>A
  • NM_020631.6:c.2867G>AMANE SELECT
  • NM_198681.4:c.2867G>A
  • NP_001036128.2:p.Arg993Lys
  • NP_001036129.1:p.Arg956Lys
  • NP_001036130.1:p.Arg956Lys
  • NP_001252521.2:p.Arg993Lys
  • NP_001252522.1:p.Arg1025Lys
  • NP_065682.2:p.Arg956Lys
  • NP_941374.3:p.Arg956Lys
  • LRG_262:g.57041G>A
  • NC_000001.10:g.6528029C>T
  • NM_020631.4:c.2867G>A
Protein change:
R1025K
Links:
dbSNP: rs773530688
NCBI 1000 Genomes Browser:
rs773530688
Molecular consequence:
  • NM_001265594.2:c.2738-71G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001042663.3:c.2978G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042664.1:c.2867G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042665.1:c.2867G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001265592.2:c.2978G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001265593.1:c.3074G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020631.6:c.2867G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198681.4:c.2867G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000227712EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Feb 13, 2015)
germlineclinical testing

Citation Link,

SCV000293956GeneDxcriteria provided, single submitter
Uncertain significance
(Jun 20, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000227712.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000293956.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

A variant of uncertain significance has been identified in the PLEKHG5 gene. The R956K variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The R956K variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The R956K variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar propertiess. This substitution occurs at a position that is not conserved, and in silico analysis predicts this variant likely does not alter the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Nov 27, 2021

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