NM_006164.5(NFE2L2):c.1680A>T (p.Leu560Phe) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 30, 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:: RCV003661897.2

Allele description [Variation Report for NM_006164.5(NFE2L2):c.1680A>T (p.Leu560Phe)]

NM_006164.5(NFE2L2):c.1680A>T (p.Leu560Phe)

Gene:

NFE2L2:NFE2 like bZIP transcription factor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q31.2

Genomic location:

Preferred name:

NM_006164.5(NFE2L2):c.1680A>T (p.Leu560Phe)

HGVS:

NC_000002.12:g.177230923T>A
NM_001145412.3:c.1632A>T
NM_001145413.3:c.1611A>T
NM_001313900.1:c.1632A>T
NM_001313901.1:c.1632A>T
NM_001313902.2:c.1590A>T
NM_001313903.2:c.1461A>T
NM_001313904.1:c.1380A>T
NM_006164.5:c.1680A>TMANE SELECT
NP_001138884.1:p.Leu544Phe
NP_001138885.1:p.Leu537Phe
NP_001300829.1:p.Leu544Phe
NP_001300830.1:p.Leu544Phe
NP_001300831.1:p.Leu530Phe
NP_001300832.1:p.Leu487Phe
NP_001300833.1:p.Leu460Phe
NP_006155.2:p.Leu560Phe
NC_000002.11:g.178095651T>A

Protein change:

L460F

Molecular consequence:

NM_001145412.3:c.1632A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001145413.3:c.1611A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001313900.1:c.1632A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001313901.1:c.1632A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001313902.2:c.1590A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001313903.2:c.1461A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001313904.1:c.1380A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006164.5:c.1680A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Mus musculus immunoglobulin joining chain (Jchain), mRNA
Mus musculus immunoglobulin joining chain (Jchain), mRNA
gi|2207981724|ref|NM_152839.4|

Nucleotide
Contraceptives, Oral, Hormonal [Pharmacological Action]
Contraceptives, Oral, Hormonal [Pharmacological Action]

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004375551	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 30, 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

SCV004375551

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 30, 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, SCV004375551.1

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

Description

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 expected to disrupt NFE2L2 protein function. This variant has not been reported in the literature in individuals affected with NFE2L2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 560 of the NFE2L2 protein (p.Leu560Phe).

#	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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