NM_000399.5(EGR2):c.457A>C (p.Thr153Pro) AND not provided

Clinical significance:Uncertain significance

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001356784.1

Allele description [Variation Report for NM_000399.5(EGR2):c.457A>C (p.Thr153Pro)]

NM_000399.5(EGR2):c.457A>C (p.Thr153Pro)

Gene:
EGR2:early growth response 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q21.3
Genomic location:
Preferred name:
NM_000399.5(EGR2):c.457A>C (p.Thr153Pro)
HGVS:
  • NC_000010.11:g.62814181T>G
  • NG_008936.2:g.110720A>C
  • NM_000399.5:c.457A>CMANE SELECT
  • NM_001136177.3:c.457A>C
  • NM_001136178.2:c.457A>C
  • NM_001136179.3:c.307A>C
  • NM_001321037.2:c.307A>C
  • NP_000390.2:p.Thr153Pro
  • NP_001129649.1:p.Thr153Pro
  • NP_001129650.1:p.Thr153Pro
  • NP_001129651.1:p.Thr103Pro
  • NP_001307966.1:p.Thr103Pro
  • LRG_239t1:c.457A>C
  • LRG_239:g.110720A>C
  • NC_000010.10:g.64573941T>G
  • NM_000399.3:c.457A>C
Protein change:
T103P
Links:
dbSNP: rs202183386
NCBI 1000 Genomes Browser:
rs202183386
Molecular consequence:
  • NM_000399.5:c.457A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136177.3:c.457A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136178.2:c.457A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136179.3:c.307A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321037.2:c.307A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001552046Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001552046.1

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

Description

The EGR2 p.Thr103Pro variant was not identified in the literature but was identified in dbSNP (ID: rs202183386) and ClinVar (classified as likely benign by Invitae). The variant was identified in control databases in 53 of 282632 chromosomes at a frequency of 0.0001875 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Ashkenazi Jewish in 41 of 10358 chromosomes (freq: 0.003958), Other in 1 of 7216 chromosomes (freq: 0.000139), European (non-Finnish) in 10 of 129006 chromosomes (freq: 0.000078) and African in 1 of 24938 chromosomes (freq: 0.00004), but was not observed in the Latino, East Asian, European (Finnish), or South Asian populations. The p.Thr103 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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

Last Updated: Nov 27, 2021

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