NM_006164.5(NFE2L2):c.892A>G (p.Ser298Gly) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 9, 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:: RCV003848828.2

Allele description [Variation Report for NM_006164.5(NFE2L2):c.892A>G (p.Ser298Gly)]

NM_006164.5(NFE2L2):c.892A>G (p.Ser298Gly)

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.892A>G (p.Ser298Gly)

HGVS:

NC_000002.12:g.177231711T>C
NM_001145412.3:c.844A>G
NM_001145413.3:c.823A>G
NM_001313900.1:c.844A>G
NM_001313901.1:c.844A>G
NM_001313902.2:c.802A>G
NM_001313903.2:c.673A>G
NM_001313904.1:c.592A>G
NM_006164.3:c.892A>G
NM_006164.5:c.892A>GMANE SELECT
NP_001138884.1:p.Ser282Gly
NP_001138885.1:p.Ser275Gly
NP_001300829.1:p.Ser282Gly
NP_001300830.1:p.Ser282Gly
NP_001300831.1:p.Ser268Gly
NP_001300832.1:p.Ser225Gly
NP_001300833.1:p.Ser198Gly
NP_006155.2:p.Ser298Gly
NC_000002.11:g.178096439T>C

Protein change:

S198G

Molecular consequence:

NM_001145412.3:c.844A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001145413.3:c.823A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001313900.1:c.844A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001313901.1:c.844A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001313902.2:c.802A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001313903.2:c.673A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001313904.1:c.592A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006164.5:c.892A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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cytochrome b (mitochondrion) [Cheirogaleus medius]
cytochrome b (mitochondrion) [Cheirogaleus medius]
gi|2282573770|ref|YP_010449150.1|

Protein
putative Polycomb group protein ASXL2 isoform 3 [Homo sapiens]
putative Polycomb group protein ASXL2 isoform 3 [Homo sapiens]
gi|1607220055|ref|NP_001356276.1|

Protein
Uncultured Acinetobacter sp. clone HYX174 16S ribosomal RNA gene, partial sequen...
Uncultured Acinetobacter sp. clone HYX174 16S ribosomal RNA gene, partial sequence
gi|428230527|gb|JX865296.1|

Nucleotide
PREDICTED: Homo sapiens neuron navigator 2 (NAV2), transcript variant X31, mRNA
PREDICTED: Homo sapiens neuron navigator 2 (NAV2), transcript variant X31, mRNA
gi|2462528536|ref|XM_054370400.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004648534	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 9, 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

SCV004648534

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 9, 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, SCV004648534.1

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

Description

This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 298 of the NFE2L2 protein (p.Ser298Gly). This variant is present in population databases (rs774940995, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with NFE2L2-related conditions. 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 NFE2L2 protein function. 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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