NM_052867.4(NALCN):c.1013C>T (p.Ser338Leu) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jun 23, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002469585.3

Allele description [Variation Report for NM_052867.4(NALCN):c.1013C>T (p.Ser338Leu)]

NM_052867.4(NALCN):c.1013C>T (p.Ser338Leu)

Gene:

NALCN:sodium leak channel, non-selective [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q33.1

Genomic location:

Preferred name:

NM_052867.4(NALCN):c.1013C>T (p.Ser338Leu)

HGVS:

NC_000013.11:g.101292024G>A
NG_053176.1:g.130183C>T
NM_001350748.2:c.1013C>T
NM_001350749.2:c.1013C>T
NM_001350750.2:c.1013C>T
NM_001350751.2:c.1013C>T
NM_052867.4:c.1013C>TMANE SELECT
NP_001337677.1:p.Ser338Leu
NP_001337678.1:p.Ser338Leu
NP_001337679.1:p.Ser338Leu
NP_001337680.1:p.Ser338Leu
NP_443099.1:p.Ser338Leu
NC_000013.10:g.101944375G>A
NM_052867.2:c.1013C>T

Protein change:

S338L

Molecular consequence:

NM_001350748.2:c.1013C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350749.2:c.1013C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350750.2:c.1013C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350751.2:c.1013C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_052867.4:c.1013C>T - 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
SCV002765359	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jun 13, 2022)	germline	clinical testing	Citation Link,
SCV004634476	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 23, 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

SCV002765359

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jun 13, 2022)

germline

clinical testing

Citation Link,

SCV004634476

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 23, 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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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 GeneDx, SCV002765359.1

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

Description

In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004634476.1

#	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 not expected to disrupt NALCN protein function. ClinVar contains an entry for this variant (Variation ID: 1804284). This variant has not been reported in the literature in individuals affected with NALCN-related conditions. This variant is present in population databases (rs773688637, gnomAD 0.01%). This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 338 of the NALCN protein (p.Ser338Leu).

#	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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