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NM_005670.4(EPM2A):c.11G>A (p.Arg4His) AND Progressive myoclonic epilepsy

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 30, 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:
RCV003089502.3

Allele description [Variation Report for NM_005670.4(EPM2A):c.11G>A (p.Arg4His)]

NM_005670.4(EPM2A):c.11G>A (p.Arg4His)

Genes:
LOC129997381:ATAC-STARR-seq lymphoblastoid silent region 17642 [Gene]
EPM2A-DT:EPM2A divergent transcript [Gene - HGNC]
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.11G>A (p.Arg4His)
HGVS:
  • NC_000006.12:g.145735488C>T
  • NG_012832.3:g.5535G>A
  • NM_001018041.2:c.11G>A
  • NM_001360057.2:c.11G>A
  • NM_001360064.2:c.-114+420G>A
  • NM_001360071.2:c.-659G>A
  • NM_001368129.2:c.-613G>A
  • NM_001368130.1:c.11G>A
  • NM_001368131.1:c.-357G>A
  • NM_005670.4:c.11G>AMANE SELECT
  • NP_001018051.1:p.Arg4His
  • NP_001346986.1:p.Arg4His
  • NP_001355059.1:p.Arg4His
  • NP_005661.1:p.Arg4His
  • NC_000006.11:g.146056624C>T
  • NG_012832.2:g.5368G>A
  • NR_153397.1:n.33G>A
Protein change:
R4H
Molecular consequence:
  • NM_001360071.2:c.-659G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368129.2:c.-613G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368131.1:c.-357G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001360064.2:c.-114+420G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001018041.2:c.11G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001360057.2:c.11G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368130.1:c.11G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005670.4:c.11G>A - 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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003474858Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 30, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV003474858.2

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

Description

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 4 of the EPM2A protein (p.Arg4His). 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: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with EPM2A-related conditions. This variant is not present in population databases (gnomAD no frequency).

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

Last Updated: Sep 29, 2024