NM_000335.5(SCN5A):c.50C>T (p.Thr17Ile) AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 3, 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:: RCV003658894.1

Allele description

NM_000335.5(SCN5A):c.50C>T (p.Thr17Ile)

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.50C>T (p.Thr17Ile)

HGVS:

NC_000003.12:g.38633258G>A
NG_008934.1:g.21415C>T
NM_000335.5:c.50C>TMANE SELECT
NM_001099404.2:c.50C>T
NM_001099405.2:c.50C>T
NM_001160160.2:c.50C>T
NM_001160161.2:c.50C>T
NM_001354701.2:c.50C>T
NM_001407185.1:c.50C>T
NM_001407186.1:c.50C>T
NM_001407187.1:c.50C>T
NM_198056.3:c.50C>T
NP_000326.2:p.Thr17Ile
NP_000326.2:p.Thr17Ile
NP_001092874.1:p.Thr17Ile
NP_001092874.1:p.Thr17Ile
NP_001092875.1:p.Thr17Ile
NP_001153632.1:p.Thr17Ile
NP_001153633.1:p.Thr17Ile
NP_001341630.1:p.Thr17Ile
NP_001394114.1:p.Thr17Ile
NP_001394115.1:p.Thr17Ile
NP_001394116.1:p.Thr17Ile
NP_932173.1:p.Thr17Ile
NP_932173.1:p.Thr17Ile
LRG_289t1:c.50C>T
LRG_289t2:c.50C>T
LRG_289t3:c.50C>T
LRG_289:g.21415C>T
LRG_289p1:p.Thr17Ile
LRG_289p2:p.Thr17Ile
LRG_289p3:p.Thr17Ile
NC_000003.11:g.38674749G>A
NM_000335.4:c.50C>T
NM_001099404.1:c.50C>T
NM_198056.2:c.50C>T
NR_176299.1:n.259C>T

Protein change:

T17I

Molecular consequence:

NM_000335.5:c.50C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.50C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.50C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.50C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.50C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.50C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407185.1:c.50C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407186.1:c.50C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407187.1:c.50C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.50C>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
SCV003512038	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 3, 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

SCV003512038

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 3, 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 Invitae, SCV003512038.2

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

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 17 of the SCN5A protein (p.Thr17Ile). This variant has not been reported in the literature in individuals affected with SCN5A-related conditions. 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive.

#	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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