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NM_000399.5(EGR2):c.500C>T (p.Pro167Leu) AND Charcot-Marie-Tooth disease, type I

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 1, 2022
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:
RCV001070072.6

Allele description [Variation Report for NM_000399.5(EGR2):c.500C>T (p.Pro167Leu)]

NM_000399.5(EGR2):c.500C>T (p.Pro167Leu)

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.500C>T (p.Pro167Leu)
HGVS:
  • NC_000010.11:g.62814138G>A
  • NG_008936.2:g.110763C>T
  • NM_000399.5:c.500C>TMANE SELECT
  • NM_001136177.3:c.500C>T
  • NM_001136178.2:c.500C>T
  • NM_001136179.3:c.350C>T
  • NM_001321037.2:c.350C>T
  • NP_000390.2:p.Pro167Leu
  • NP_001129649.1:p.Pro167Leu
  • NP_001129650.1:p.Pro167Leu
  • NP_001129651.1:p.Pro117Leu
  • NP_001307966.1:p.Pro117Leu
  • LRG_239t1:c.500C>T
  • LRG_239:g.110763C>T
  • NC_000010.10:g.64573898G>A
  • NM_000399.3:c.500C>T
Protein change:
P117L
Links:
dbSNP: rs1842200895
NCBI 1000 Genomes Browser:
rs1842200895
Molecular consequence:
  • NM_000399.5:c.500C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136177.3:c.500C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136178.2:c.500C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136179.3:c.350C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321037.2:c.350C>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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001235281Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Sep 1, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Comprehensive genetic sequence and copy number analysis for Charcot-Marie-Tooth disease in a Canadian cohort of 2517 patients.

Volodarsky M, Kerkhof J, Stuart A, Levy M, Brady LI, Tarnopolsky M, Lin H, Ainsworth P, Sadikovic B.

J Med Genet. 2021 Apr;58(4):284-288. doi: 10.1136/jmedgenet-2019-106641. Epub 2020 May 6.

PubMed [citation]
PMID:
32376792

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, SCV001235281.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available"). ClinVar contains an entry for this variant (Variation ID: 863169). This missense change has been observed in individual(s) with clinical features of EGR2-related conditions (PMID: 32376792). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 167 of the EGR2 protein (p.Pro167Leu). 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