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NM_005670.4(EPM2A):c.88G>A (p.Gly30Arg) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 31, 2014
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:
RCV000187405.1

Allele description [Variation Report for NM_005670.4(EPM2A):c.88G>A (p.Gly30Arg)]

NM_005670.4(EPM2A):c.88G>A (p.Gly30Arg)

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.88G>A (p.Gly30Arg)
Other names:
p.G30R:GGG>AGG
HGVS:
  • NC_000006.12:g.145735411C>T
  • NG_012832.2:g.5445G>A
  • NM_001018041.2:c.88G>A
  • NM_001360057.2:c.88G>A
  • NM_001360064.2:c.-114+497G>A
  • NM_001360071.2:c.-582G>A
  • NM_001368129.2:c.-536G>A
  • NM_001368130.1:c.88G>A
  • NM_001368131.1:c.-280G>A
  • NM_005670.4:c.88G>AMANE SELECT
  • NP_001018051.1:p.Gly30Arg
  • NP_001346986.1:p.Gly30Arg
  • NP_001355059.1:p.Gly30Arg
  • NP_005661.1:p.Gly30Arg
  • NC_000006.11:g.146056547C>T
  • NG_012832.1:g.5445G>A
  • NM_005670.3:c.88G>A
Protein change:
G30R
Links:
dbSNP: rs796052434
NCBI 1000 Genomes Browser:
rs796052434
Molecular consequence:
  • NM_001360071.2:c.-582G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368129.2:c.-536G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368131.1:c.-280G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001360064.2:c.-114+497G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001018041.2:c.88G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001360057.2:c.88G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368130.1:c.88G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005670.4:c.88G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000240992GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Mar 31, 2014) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000240992.11

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

Description

p.Gly30Arg (GGG>AGG): c.88 G>A in exon 1 of the EPM2A gene (NM_005670.3). The G30R variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 300 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 G30R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. It alters a conserved position in the CBM20 domain of the protein, and missense mutations at nearby residues (S25P, E28K, W32G) have been reported in association with epilepsy, supporting the functional importance of this region of the protein. Furthermore, in silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, this variant is a strong candidate for a pathogenic mutation; however, the possibility that it is a benign variant cannot be excluded. The variant is found in EPILEPSY panel(s).

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

Last Updated: Oct 14, 2023