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NM_000399.5(EGR2):c.644C>T (p.Thr215Met) AND EGR2-related disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 20, 2023
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003955388.2

Allele description [Variation Report for NM_000399.5(EGR2):c.644C>T (p.Thr215Met)]

NM_000399.5(EGR2):c.644C>T (p.Thr215Met)

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.644C>T (p.Thr215Met)
HGVS:
  • NC_000010.11:g.62813994G>A
  • NG_008936.2:g.110907C>T
  • NM_000399.4:c.644C>T
  • NM_000399.5:c.644C>TMANE SELECT
  • NM_001136177.3:c.644C>T
  • NM_001136178.2:c.644C>T
  • NM_001136179.3:c.494C>T
  • NM_001321037.2:c.494C>T
  • NP_000390.2:p.Thr215Met
  • NP_001129649.1:p.Thr215Met
  • NP_001129650.1:p.Thr215Met
  • NP_001129651.1:p.Thr165Met
  • NP_001307966.1:p.Thr165Met
  • LRG_239t1:c.644C>T
  • LRG_239:g.110907C>T
  • NC_000010.10:g.64573754G>A
  • NM_000399.3:c.644C>T
Protein change:
T165M
Links:
dbSNP: rs139147487
NCBI 1000 Genomes Browser:
rs139147487
Molecular consequence:
  • NM_000399.5:c.644C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136177.3:c.644C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136178.2:c.644C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136179.3:c.494C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321037.2:c.494C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
EGR2-related disorder
Synonyms:
EGR2-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004773629PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Uncertain significance
(Dec 20, 2023) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004773629.2

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

Description

The EGR2 c.644C>T variant is predicted to result in the amino acid substitution p.Thr215Met. This variant was reported in two individuals from a Charcot-Marie-Tooth disease cohort (Supplementary Table 2 in Volodarsky et al. 2021. PubMed ID: 32376792). This variant is reported in 0.11% of alleles in individuals of European (Non-Finnish) descent in gnomAD, which may be too frequent for a disease-causing variant in EGR2. This variant has conflicting interpretations in ClinVar ranging from uncertain to likely benign (https://preview.ncbi.nlm.nih.gov/clinvar/variation/246013/). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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

Last Updated: Oct 26, 2024