NM_001144967.3(NEDD4L):c.1535G>A (p.Arg512Gln) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 29, 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:: RCV000810228.7

Allele description [Variation Report for NM_001144967.3(NEDD4L):c.1535G>A (p.Arg512Gln)]

NM_001144967.3(NEDD4L):c.1535G>A (p.Arg512Gln)

Gene:

NEDD4L:NEDD4 like E3 ubiquitin protein ligase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18q21.31

Genomic location:

Preferred name:

NM_001144967.3(NEDD4L):c.1535G>A (p.Arg512Gln)

HGVS:

NC_000018.10:g.58343063G>A
NG_029954.1:g.303686G>A
NM_001144964.1:c.1172G>A
NM_001144965.2:c.1172G>A
NM_001144966.3:c.1172G>A
NM_001144967.3:c.1535G>AMANE SELECT
NM_001144968.2:c.1511G>A
NM_001144969.2:c.1451G>A
NM_001144970.3:c.1112G>A
NM_001144971.2:c.1112G>A
NM_001243960.2:c.1343G>A
NM_015277.6:c.1475G>A
NP_001138436.1:p.Arg391Gln
NP_001138437.1:p.Arg391Gln
NP_001138438.1:p.Arg391Gln
NP_001138439.1:p.Arg512Gln
NP_001138440.1:p.Arg504Gln
NP_001138441.1:p.Arg484Gln
NP_001138442.1:p.Arg371Gln
NP_001138443.1:p.Arg371Gln
NP_001230889.1:p.Arg448Gln
NP_056092.2:p.Arg492Gln
NC_000018.9:g.56010295G>A
NM_015277.5:c.1475G>A

Protein change:

R371Q

Links:

dbSNP: rs1365042367

NCBI 1000 Genomes Browser:

rs1365042367

Molecular consequence:

NM_001144964.1:c.1172G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001144965.2:c.1172G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001144966.3:c.1172G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001144967.3:c.1535G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001144968.2:c.1511G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001144969.2:c.1451G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001144970.3:c.1112G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001144971.2:c.1112G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001243960.2:c.1343G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015277.6:c.1475G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000950421	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 29, 2022)	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

SCV000950421

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 29, 2022)

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, SCV000950421.4

#	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 not expected to disrupt NEDD4L protein function. ClinVar contains an entry for this variant (Variation ID: 654299). This variant has not been reported in the literature in individuals affected with NEDD4L-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 492 of the NEDD4L protein (p.Arg492Gln).

#	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