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NM_000399.5(EGR2):c.1314del (p.Ser439fs) AND Charcot-Marie-Tooth disease, type I

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 4, 2019
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:
RCV001214430.7

Allele description [Variation Report for NM_000399.5(EGR2):c.1314del (p.Ser439fs)]

NM_000399.5(EGR2):c.1314del (p.Ser439fs)

Gene:
EGR2:early growth response 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
10q21.3
Genomic location:
Preferred name:
NM_000399.5(EGR2):c.1314del (p.Ser439fs)
HGVS:
  • NC_000010.11:g.62813328del
  • NG_008936.2:g.111577del
  • NM_000399.5:c.1314delMANE SELECT
  • NM_001136177.3:c.1314del
  • NM_001136178.2:c.1314del
  • NM_001136179.3:c.1164del
  • NM_001321037.2:c.1164del
  • NP_000390.2:p.Ser439fs
  • NP_001129649.1:p.Ser439fs
  • NP_001129650.1:p.Ser439fs
  • NP_001129651.1:p.Ser389fs
  • NP_001307966.1:p.Ser389fs
  • LRG_239t1:c.1314del
  • LRG_239:g.111577del
  • NC_000010.10:g.64573084del
  • NC_000010.10:g.64573088del
  • NM_000399.3:c.1314del
Protein change:
S389fs
Links:
dbSNP: rs1842160144
NCBI 1000 Genomes Browser:
rs1842160144
Molecular consequence:
  • NM_000399.5:c.1314del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001136177.3:c.1314del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001136178.2:c.1314del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001136179.3:c.1164del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001321037.2:c.1164del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Charcot-Marie-Tooth disease, type I (CMT1)
Synonyms:
Charcot-Marie-Tooth Neuropathy Type 1; Hereditary Motor and Sensory Neuropathy 1; Charcot-Marie-Tooth, Type 1
Identifiers:
MONDO: MONDO:0019011; MedGen: C0751036

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001386112Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(May 4, 2019)
germlineclinical testing

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

Summary from all submissions

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

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001386112.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant has not been reported in the literature in individuals with EGR2-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change results in a frameshift in the EGR2 gene (p.Ser439Leufs*96). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 38 amino acids of the EGR2 protein and extend the protein by an additional 57 amino acids. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024