NM_020631.6(PLEKHG5):c.1616C>T (p.Ala539Val) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 13, 2019
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:: RCV001001707.8

Allele description [Variation Report for NM_020631.6(PLEKHG5):c.1616C>T (p.Ala539Val)]

NM_020631.6(PLEKHG5):c.1616C>T (p.Ala539Val)

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.1616C>T (p.Ala539Val)

HGVS:

NC_000001.11:g.6470570G>A
NG_007978.1:g.54440C>T
NG_029910.1:g.626C>T
NM_001042663.3:c.1727C>T
NM_001042664.2:c.1616C>T
NM_001042665.2:c.1616C>T
NM_001265592.2:c.1727C>T
NM_001265593.2:c.1823C>T
NM_001265594.3:c.1616C>T
NM_020631.6:c.1616C>TMANE SELECT
NM_198681.4:c.1616C>T
NP_001036128.2:p.Ala576Val
NP_001036129.1:p.Ala539Val
NP_001036129.1:p.Ala539Val
NP_001036130.1:p.Ala539Val
NP_001036130.1:p.Ala539Val
NP_001252521.2:p.Ala576Val
NP_001252522.1:p.Ala608Val
NP_001252522.1:p.Ala608Val
NP_001252523.1:p.Ala539Val
NP_001252523.1:p.Ala539Val
NP_065682.2:p.Ala539Val
NP_065682.2:p.Ala539Val
NP_941374.3:p.Ala539Val
LRG_262t1:c.1616C>T
LRG_262:g.54440C>T
LRG_262p1:p.Ala539Val
NC_000001.10:g.6530630G>A
NM_001042664.1:c.1616C>T
NM_001042665.1:c.1616C>T
NM_001265593.1:c.1823C>T
NM_001265594.2:c.1616C>T
NM_020631.3:c.1616C>T
NM_020631.4:c.1616C>T

Protein change:

A539V

Links:

dbSNP: rs370515061

NCBI 1000 Genomes Browser:

rs370515061

Molecular consequence:

NM_001042663.3:c.1727C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001042664.2:c.1616C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001042665.2:c.1616C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001265592.2:c.1727C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001265593.2:c.1823C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001265594.3:c.1616C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_020631.6:c.1616C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_198681.4:c.1616C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001159284	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Uncertain significance (Mar 13, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001159284

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Uncertain significance
(Mar 13, 2019)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001159284.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The p.Ala539Val variant (rs370515061) has not been reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. This variant is listed in the Genome Aggregation Database (gnomAD) with an overall population frequency of 0.04 percent (identified on 45 out of 100,098 chromosomes) and has been reported to the ClinVar database (Variation ID: 194553). The alanine at position 539 is moderately conserved and computational analyses of the effects of the p.Ala539Val variant on protein structure and function is neutral (SIFT: tolerated, PolyPhen-2: benign). Altogether, there is not enough evidence to classify the p.Ala539Val variant with certainty.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine