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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001386112	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 4, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001386112

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 4, 2019)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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