NM_001144967.3(NEDD4L):c.2614G>C (p.Gly872Arg) AND Periventricular nodular heterotopia 7

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 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:: RCV003459012.1

Allele description [Variation Report for NM_001144967.3(NEDD4L):c.2614G>C (p.Gly872Arg)]

NM_001144967.3(NEDD4L):c.2614G>C (p.Gly872Arg)

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.2614G>C (p.Gly872Arg)

HGVS:

NC_000018.10:g.58389151G>C
NG_029954.1:g.349774G>C
NM_001144964.1:c.2251G>C
NM_001144965.2:c.2251G>C
NM_001144966.3:c.2251G>C
NM_001144967.3:c.2614G>CMANE SELECT
NM_001144968.2:c.2590G>C
NM_001144969.2:c.2530G>C
NM_001144970.3:c.2191G>C
NM_001144971.2:c.2191G>C
NM_001243960.2:c.2422G>C
NM_015277.6:c.2554G>C
NP_001138436.1:p.Gly751Arg
NP_001138437.1:p.Gly751Arg
NP_001138438.1:p.Gly751Arg
NP_001138439.1:p.Gly872Arg
NP_001138440.1:p.Gly864Arg
NP_001138441.1:p.Gly844Arg
NP_001138442.1:p.Gly731Arg
NP_001138443.1:p.Gly731Arg
NP_001230889.1:p.Gly808Arg
NP_056092.2:p.Gly852Arg
NC_000018.9:g.56056383G>C

Protein change:

G731R

Molecular consequence:

NM_001144964.1:c.2251G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001144965.2:c.2251G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001144966.3:c.2251G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001144967.3:c.2614G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001144968.2:c.2590G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001144969.2:c.2530G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001144970.3:c.2191G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001144971.2:c.2191G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001243960.2:c.2422G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_015277.6:c.2554G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Periventricular nodular heterotopia 7 (PVNH7)
Identifiers:: MONDO: MONDO:0014966; MedGen: C4310669; OMIM: 617201

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004177165	Clinical Genomics Laboratory, Washington University in St. Louis	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 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

SCV004177165

Clinical Genomics Laboratory, Washington University in St. Louis

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Clinical Genomics Laboratory, Washington University in St. Louis, SCV004177165.1

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

Description

The NEDD4L c.2614G>C (p.Gly872Arg) variant, to our knowledge, has not been reported in the medical literature and is absent from the general population (gnomAD v.2.1.1), indicating it is not a common variant. This codon occurs in the HECT domain and exchanges a neutral non-polar glycine for a positively charged arginine. However, computational predictors are uncertain as to the impact of this variant on NEDD4L function. Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of this variant is uncertain at this time.

#	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: Dec 30, 2023

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