NM_020631.5(PLEKHG5):c.1826C>A (p.Thr609Lys) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Aug 3, 2015)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000236440.1

Allele description [Variation Report for NM_020631.5(PLEKHG5):c.1826C>A (p.Thr609Lys)]

NM_020631.5(PLEKHG5):c.1826C>A (p.Thr609Lys)

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_020631.5(PLEKHG5):c.1826C>A (p.Thr609Lys)
HGVS:
  • NC_000001.11:g.6469651G>T
  • NG_007978.1:g.55359C>A
  • NG_029910.1:g.1545C>A
  • NM_001042663.2:c.1994C>A
  • NM_001042664.1:c.1826C>A
  • NM_001042665.1:c.1826C>A
  • NM_001265592.1:c.2063C>A
  • NM_001265593.1:c.2033C>A
  • NM_001265594.2:c.1826C>A
  • NM_020631.5:c.1826C>A
  • NM_198681.3:c.2057C>A
  • NP_001036128.1:p.Thr665Lys
  • NP_001036129.1:p.Thr609Lys
  • NP_001036130.1:p.Thr609Lys
  • NP_001252521.1:p.Thr688Lys
  • NP_001252522.1:p.Thr678Lys
  • NP_001252523.1:p.Thr609Lys
  • NP_065682.2:p.Thr609Lys
  • NP_941374.2:p.Thr686Lys
  • LRG_262:g.55359C>A
  • NC_000001.10:g.6529711G>T
  • NM_020631.4:c.1826C>A
Protein change:
T609K
Links:
dbSNP: rs553151077
NCBI 1000 Genomes Browser:
rs553151077
Molecular consequence:
  • NM_001042663.2:c.1994C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042664.1:c.1826C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042665.1:c.1826C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001265592.1:c.2063C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001265593.1:c.2033C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001265594.2:c.1826C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020631.5:c.1826C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198681.3:c.2057C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000293008GeneDxcriteria provided, single submitter
Uncertain significance
(Aug 3, 2015)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000293008.10

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

Description

The T609K variant has not been published as pathogenic, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The T609K variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. However, missense variants associated with neuropathy have not been reported in this region of the protein (Stenson et al., 2014). 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: Feb 27, 2021

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