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NM_002633.3(PGM1):c.247-5810G>A AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 22, 2018
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:
RCV000578844.1

Allele description [Variation Report for NM_002633.3(PGM1):c.247-5810G>A]

NM_002633.3(PGM1):c.247-5810G>A

Gene:
PGM1:phosphoglucomutase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p31.3
Genomic location:
Preferred name:
NM_002633.3(PGM1):c.247-5810G>A
HGVS:
  • NC_000001.11:g.63623615G>A
  • NG_016966.1:g.35340G>A
  • NM_001172818.1:c.155G>A
  • NM_001172819.2:c.-345-5810G>A
  • NM_002633.3:c.247-5810G>AMANE SELECT
  • NP_001166289.1:p.Cys52Tyr
  • NC_000001.10:g.64089286G>A
  • NM_002633.2:c.247-5810G>A
Protein change:
C52Y
Links:
dbSNP: rs140738630
NCBI 1000 Genomes Browser:
rs140738630
Molecular consequence:
  • NM_001172819.2:c.-345-5810G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_002633.3:c.247-5810G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001172818.1:c.155G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000681003GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jan 22, 2018) 		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, SCV000681003.2

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

Description

The C52Y variant, present in an alternate transcript of the PGM1 gene, has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The C52Y variant is observed in 56/22848 (0.25%) alleles from individuals of African background in large population cohorts (Lek et al., 2016). The C52Y 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. In-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function. We interpret C52Y as a variant of uncertain significance.

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

Last Updated: Dec 24, 2023