NM_000399.5(EGR2):c.442C>T (p.Pro148Ser) AND Charcot-Marie-Tooth disease, type I

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 19, 2023
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:: RCV000797593.9

Allele description [Variation Report for NM_000399.5(EGR2):c.442C>T (p.Pro148Ser)]

NM_000399.5(EGR2):c.442C>T (p.Pro148Ser)

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.442C>T (p.Pro148Ser)

HGVS:

NC_000010.11:g.62814196G>A
NG_008936.2:g.110705C>T
NM_000399.5:c.442C>TMANE SELECT
NM_001136177.3:c.442C>T
NM_001136178.2:c.442C>T
NM_001136179.3:c.292C>T
NM_001321037.2:c.292C>T
NP_000390.2:p.Pro148Ser
NP_001129649.1:p.Pro148Ser
NP_001129650.1:p.Pro148Ser
NP_001129651.1:p.Pro98Ser
NP_001307966.1:p.Pro98Ser
LRG_239t1:c.442C>T
LRG_239:g.110705C>T
NC_000010.10:g.64573956G>A
NM_000399.3:c.442C>T

Protein change:

P148S

Links:

dbSNP: rs147604283

NCBI 1000 Genomes Browser:

rs147604283

Molecular consequence:

NM_000399.5:c.442C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001136177.3:c.442C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001136178.2:c.442C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001136179.3:c.292C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001321037.2:c.292C>T - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000937157	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 19, 2023)	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

SCV000937157

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 19, 2023)

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, SCV000937157.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

ClinVar contains an entry for this variant (Variation ID: 195071). 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt EGR2 protein function. This missense change has been observed in individual(s) with Charcot-Marie-Tooth disease (Invitae). This variant is present in population databases (rs147604283, gnomAD 0.06%). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 148 of the EGR2 protein (p.Pro148Ser).

#	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

ClinVar

Relating variation to medicine