NM_005670.4(EPM2A):c.487A>G (p.Asn163Asp) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 30, 2016
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:: RCV000413724.1

Allele description [Variation Report for NM_005670.4(EPM2A):c.487A>G (p.Asn163Asp)]

NM_005670.4(EPM2A):c.487A>G (p.Asn163Asp)

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.487A>G (p.Asn163Asp)

HGVS:

NC_000006.12:g.145635476T>C
NG_012832.2:g.105380A>G
NM_001018041.2:c.487A>G
NM_001360057.2:c.477-7783A>G
NM_001360064.2:c.73A>G
NM_001360071.2:c.73A>G
NM_001368129.2:c.25A>G
NM_001368130.1:c.487A>G
NM_001368131.1:c.73A>G
NM_001368132.1:c.25A>G
NM_005670.4:c.487A>GMANE SELECT
NP_001018051.1:p.Asn163Asp
NP_001346993.1:p.Asn25Asp
NP_001347000.1:p.Asn25Asp
NP_001355058.1:p.Asn9Asp
NP_001355059.1:p.Asn163Asp
NP_001355060.1:p.Asn25Asp
NP_001355061.1:p.Asn9Asp
NP_005661.1:p.Asn163Asp
NC_000006.11:g.145956612T>C
NG_012832.1:g.105380A>G
NM_005670.3:c.487A>G

Protein change:

N163D

Links:

dbSNP: rs777767978

NCBI 1000 Genomes Browser:

rs777767978

Molecular consequence:

NM_001360057.2:c.477-7783A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001018041.2:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001360064.2:c.73A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001360071.2:c.73A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368129.2:c.25A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368130.1:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368131.1:c.73A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368132.1:c.25A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_005670.4:c.487A>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
SCV000491779	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Nov 30, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000491779

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Nov 30, 2016)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000491779.1

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

Description

The N163D variant in the EPM2A gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The N163D variant was not observed in approximately 6,500 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 N163D variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is not conserved. In silico analysis predicts this variant is probably damaging to the protein structure/function. The N163D variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded.

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

Last Updated: Sep 29, 2024

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