NM_005670.4(EPM2A):c.31C>T (p.Pro11Ser) AND Progressive myoclonic epilepsy

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 22, 2022
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:: RCV000815938.8

Allele description

NM_005670.4(EPM2A):c.31C>T (p.Pro11Ser)

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.31C>T (p.Pro11Ser)

HGVS:

NC_000006.12:g.145735468G>A
NG_012832.2:g.5388C>T
NM_001018041.2:c.31C>T
NM_001360057.2:c.31C>T
NM_001360064.2:c.-114+440C>T
NM_001360071.2:c.-639C>T
NM_001368129.2:c.-593C>T
NM_001368130.1:c.31C>T
NM_001368131.1:c.-337C>T
NM_005670.4:c.31C>TMANE SELECT
NP_001018051.1:p.Pro11Ser
NP_001346986.1:p.Pro11Ser
NP_001355059.1:p.Pro11Ser
NP_005661.1:p.Pro11Ser
NC_000006.11:g.146056604G>A
NG_012832.1:g.5388C>T
NM_005670.3:c.31C>T

Protein change:

P11S

Links:

dbSNP: rs1583157330

NCBI 1000 Genomes Browser:

rs1583157330

Molecular consequence:

NM_001360071.2:c.-639C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001368129.2:c.-593C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001368131.1:c.-337C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001360064.2:c.-114+440C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001018041.2:c.31C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001360057.2:c.31C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368130.1:c.31C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_005670.4:c.31C>T - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000956418	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 22, 2022)	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

SCV000956418

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 22, 2022)

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 Invitae, SCV000956418.6

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

Description

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 output the following: SIFT: "Tolerated"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 659007). 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). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 11 of the EPM2A protein (p.Pro11Ser).

#	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: Feb 14, 2024

ClinVar

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