NM_005670.4(EPM2A):c.159C>G (p.Ala53=) AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Apr 29, 2017
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000675705.16

Allele description [Variation Report for NM_005670.4(EPM2A):c.159C>G (p.Ala53=)]

NM_005670.4(EPM2A):c.159C>G (p.Ala53=)

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.159C>G (p.Ala53=)

HGVS:

NC_000006.12:g.145735340G>C
NG_012832.2:g.5516C>G
NM_001018041.2:c.159C>G
NM_001360057.2:c.159C>G
NM_001360064.2:c.-114+568C>G
NM_001360071.2:c.-511C>G
NM_001368129.2:c.-465C>G
NM_001368130.1:c.159C>G
NM_001368131.1:c.-209C>G
NM_005670.4:c.159C>GMANE SELECT
NP_001018051.1:p.Ala53=
NP_001346986.1:p.Ala53=
NP_001355059.1:p.Ala53=
NP_005661.1:p.Ala53=
NC_000006.11:g.146056476G>C
NG_012832.1:g.5516C>G
NM_005670.3:c.159C>G
NP_005661.1:p.(=)
p.Ala53Ala

Links:

dbSNP: rs2235482

NCBI 1000 Genomes Browser:

rs2235482

Molecular consequence:

NM_001360071.2:c.-511C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001368129.2:c.-465C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001368131.1:c.-209C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001360064.2:c.-114+568C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001018041.2:c.159C>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001360057.2:c.159C>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001368130.1:c.159C>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_005670.4:c.159C>G - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000677289	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Apr 29, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000801418	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Benign (Oct 19, 2015)	unknown	clinical testing
SCV001950649	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Mar 3, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000677289

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Benign
(Apr 29, 2017)

germline

clinical testing

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

SCV000801418

Mayo Clinic Laboratories, Mayo Clinic

no assertion criteria provided

Benign
(Oct 19, 2015)

unknown

clinical testing

SCV001950649

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Mar 3, 2015)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Athena Diagnostics, SCV000677289.2

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

#	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

From Mayo Clinic Laboratories, Mayo Clinic, SCV000801418.1

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

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

From GeneDx, SCV001950649.2

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

#	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: Nov 24, 2024

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