NM_006245.4(PPP2R5D):c.1799A>G (p.Glu600Gly) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 18, 2021
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:: RCV001983318.4

Allele description [Variation Report for NM_006245.4(PPP2R5D):c.1799A>G (p.Glu600Gly)]

NM_006245.4(PPP2R5D):c.1799A>G (p.Glu600Gly)

Genes:

MEA1:male-enhanced antigen 1 [Gene - OMIM - HGNC]
PPP2R5D:protein phosphatase 2 regulatory subunit B'delta [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.1

Genomic location:

Preferred name:

NM_006245.4(PPP2R5D):c.1799A>G (p.Glu600Gly)

HGVS:

NC_000006.12:g.43011276A>G
NG_050636.1:g.31778A>G
NM_001270476.2:c.1346A>G
NM_006245.4:c.1799A>GMANE SELECT
NM_014623.4:c.*1194T>CMANE SELECT
NM_180976.3:c.1703A>G
NM_180977.3:c.1481A>G
NP_001257405.1:p.Glu449Gly
NP_006236.1:p.Glu600Gly
NP_851307.1:p.Glu568Gly
NP_851308.1:p.Glu494Gly
NC_000006.11:g.42979014A>G

Protein change:

E449G

Links:

dbSNP: rs2150284112

NCBI 1000 Genomes Browser:

rs2150284112

Molecular consequence:

NM_014623.4:c.*1194T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001270476.2:c.1346A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006245.4:c.1799A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_180976.3:c.1703A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_180977.3:c.1481A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002246800	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 18, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002246800

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 18, 2021)

germline

clinical testing

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

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

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002246800.3

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

Description

This sequence change replaces glutamic acid with glycine at codon 600 of the PPP2R5D protein (p.Glu600Gly). The glutamic acid residue is moderately conserved and there is a moderate physicochemical difference between glutamic acid and glycine. 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with PPP2R5D-related conditions. This variant is not present in population databases (ExAC no frequency).

#	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

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