NM_020631.6(PLEKHG5):c.440-2A>G AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely pathogenic(1);Uncertain significance(1) (Last evaluated: Feb 15, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000485207.5

Allele description [Variation Report for NM_020631.6(PLEKHG5):c.440-2A>G]

NM_020631.6(PLEKHG5):c.440-2A>G

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.440-2A>G
HGVS:
  • NC_000001.11:g.6474166T>C
  • NG_007978.1:g.50844A>G
  • NM_001042663.3:c.551-2A>G
  • NM_001042664.1:c.440-2A>G
  • NM_001042665.1:c.440-2A>G
  • NM_001265592.2:c.551-2A>G
  • NM_001265593.1:c.647-2A>G
  • NM_001265594.2:c.440-2A>G
  • NM_020631.6:c.440-2A>GMANE SELECT
  • NM_198681.4:c.440-2A>G
  • LRG_262:g.50844A>G
  • NC_000001.10:g.6534226T>C
  • NM_020631.4:c.440-2A>G
  • NM_198681.3:c.671-2A>G
Links:
dbSNP: rs144750655
NCBI 1000 Genomes Browser:
rs144750655
Molecular consequence:
  • NM_001042663.3:c.551-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001042664.1:c.440-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001042665.1:c.440-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001265592.2:c.551-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001265593.1:c.647-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001265594.2:c.440-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_020631.6:c.440-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_198681.4:c.440-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
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
SCV000573584GeneDxcriteria provided, single submitter
Uncertain significance
(Feb 15, 2021)
germlineclinical testing

Citation Link,

SCV001713780Mayo Clinic Laboratories,Mayo Cliniccriteria provided, single submitter
Likely pathogenic
(Aug 5, 2019)
germlineclinical testing

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

SCV002024682PerkinElmer Genomicsno assertion criteria providedLikely pathogenic
(Oct 14, 2019)
germlineclinical testing

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From GeneDx, SCV000573584.5

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

Description

Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 31589614)

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

From Mayo Clinic Laboratories,Mayo Clinic, SCV001713780.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

PVS1, PM2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From PerkinElmer Genomics, SCV002024682.1

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

Last Updated: Dec 4, 2021

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