NM_000290.4(PGAM2):c.707A>C (p.Glu236Ala) AND Glycogen storage disease type X

Clinical significance:Likely benign (Last evaluated: Jul 12, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000509297.4

Allele description [Variation Report for NM_000290.4(PGAM2):c.707A>C (p.Glu236Ala)]

NM_000290.4(PGAM2):c.707A>C (p.Glu236Ala)

Genes:
DBNL:drebrin like [Gene - OMIM - HGNC]
PGAM2:phosphoglycerate mutase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p13
Genomic location:
Preferred name:
NM_000290.4(PGAM2):c.707A>C (p.Glu236Ala)
HGVS:
  • NC_000007.14:g.44062819T>G
  • NG_013016.1:g.7769A>C
  • NM_000290.4:c.707A>CMANE SELECT
  • NM_001014436.3:c.*1903T>GMANE SELECT
  • NM_001122956.2:c.*1903T>G
  • NM_001284313.2:c.*1903T>G
  • NM_001362723.2:c.*1903T>G
  • NM_014063.7:c.*1903T>G
  • NP_000281.2:p.Glu236Ala
  • NC_000007.13:g.44102418T>G
  • NM_000290.3:c.707A>C
Protein change:
E236A
Links:
dbSNP: rs140230479
NCBI 1000 Genomes Browser:
rs140230479
Molecular consequence:
  • NM_001014436.3:c.*1903T>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001122956.2:c.*1903T>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001284313.2:c.*1903T>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001362723.2:c.*1903T>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_014063.7:c.*1903T>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_000290.4:c.707A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Glycogen storage disease type X (GSD10)
Synonyms:
GSD X; PHOSPHOGLYCERATE MUTASE, MUSCLE, DEFICIENCY OF; Dimauro disease; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009865; MedGen: C0268149; Orphanet: 97234; OMIM: 261670

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000607023GenomeConnect, ClinGenno assertion providednot providedunknownphenotyping only

SCV001107608Invitaecriteria provided, single submitter
Likely benign
(Jul 12, 2020)
germlineclinical testing

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

SCV001325561Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Jan 13, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedphenotyping only

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From GenomeConnect, ClinGen, SCV000607023.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedphenotyping onlynot provided

Description

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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

From Invitae, SCV001107608.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV001325561.1

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

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

Last Updated: Oct 6, 2021

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