NM_005670.4(EPM2A):c.640C>G (p.Pro214Ala) AND Progressive myoclonic epilepsy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 28, 2017
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:: RCV000525708.7

Allele description [Variation Report for NM_005670.4(EPM2A):c.640C>G (p.Pro214Ala)]

NM_005670.4(EPM2A):c.640C>G (p.Pro214Ala)

Gene:

EPM2A:EPM2A glucan phosphatase, laforin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q24.3

Genomic location:

Preferred name:

NM_005670.4(EPM2A):c.640C>G (p.Pro214Ala)

HGVS:

NC_000006.12:g.145635323G>C
NG_012832.2:g.105533C>G
NM_001018041.2:c.640C>G
NM_001360057.2:c.477-7630C>G
NM_001360064.2:c.226C>G
NM_001360071.2:c.226C>G
NM_001368129.2:c.178C>G
NM_001368130.1:c.640C>G
NM_001368131.1:c.226C>G
NM_001368132.1:c.178C>G
NM_005670.4:c.640C>GMANE SELECT
NP_001018051.1:p.Pro214Ala
NP_001346993.1:p.Pro76Ala
NP_001347000.1:p.Pro76Ala
NP_001355058.1:p.Pro60Ala
NP_001355059.1:p.Pro214Ala
NP_001355060.1:p.Pro76Ala
NP_001355061.1:p.Pro60Ala
NP_005661.1:p.Pro214Ala
NC_000006.11:g.145956459G>C
NG_012832.1:g.105533C>G
NM_005670.3:c.640C>G

Protein change:

P214A

Links:

dbSNP: rs1278542056

NCBI 1000 Genomes Browser:

rs1278542056

Molecular consequence:

NM_001360057.2:c.477-7630C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001018041.2:c.640C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001360064.2:c.226C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001360071.2:c.226C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368129.2:c.178C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368130.1:c.640C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368131.1:c.226C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368132.1:c.178C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_005670.4:c.640C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Progressive myoclonic epilepsy
Synonyms:: Myoclonic Epilepsies, Progressive; Familial progressive myoclonic epilepsy; Progressive myoclonus epilepsy; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0020074; MedGen: C0751778; Orphanet: 308; OMIM: PS254800

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000636477	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 28, 2017)	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

SCV000636477

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 28, 2017)

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, SCV000636477.4

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

Description

In summary, this variant is a novel missense change that is not predicted to affect protein function. There is no indication that it causes disease, but the available evidence is currently insufficient to prove that conclusively. 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 output the following: SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C25". The alanine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a EPM2A-related disease. This sequence change replaces proline with alanine at codon 214 of the EPM2A protein (p.Pro214Ala). The proline residue is highly conserved and there is a small physicochemical difference between proline and alanine.

#	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