NM_000335.5(SCN5A):c.59C>T (p.Ser20Phe) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 29, 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:: RCV003541504.1

Allele description

NM_000335.5(SCN5A):c.59C>T (p.Ser20Phe)

Gene:

SCN5A:sodium voltage-gated channel alpha subunit 5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000335.5(SCN5A):c.59C>T (p.Ser20Phe)

HGVS:

NC_000003.12:g.38633249G>A
NG_008934.1:g.21424C>T
NM_000335.5:c.59C>TMANE SELECT
NM_001099404.2:c.59C>T
NM_001099405.2:c.59C>T
NM_001160160.2:c.59C>T
NM_001160161.2:c.59C>T
NM_001354701.2:c.59C>T
NM_198056.3:c.59C>T
NP_000326.2:p.Ser20Phe
NP_001092874.1:p.Ser20Phe
NP_001092875.1:p.Ser20Phe
NP_001153632.1:p.Ser20Phe
NP_001153633.1:p.Ser20Phe
NP_001341630.1:p.Ser20Phe
NP_932173.1:p.Ser20Phe
LRG_289:g.21424C>T
NC_000003.11:g.38674740G>A

Protein change:

S20F

Links:

dbSNP: rs369275887

NCBI 1000 Genomes Browser:

rs369275887

Molecular consequence:

NM_000335.5:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.59C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.59C>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
SCV002169197	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 29, 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

SCV002169197

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 29, 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 Invitae, SCV002169197.3

#	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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 1405082). This variant has not been reported in the literature in individuals affected with SCN5A-related conditions. This variant is present in population databases (rs369275887, gnomAD 0.007%). This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 20 of the SCN5A protein (p.Ser20Phe).

#	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 16, 2024

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Relating variation to medicine