NM_174934.4(SCN4B):c.305C>A (p.Thr102Asn) AND Long QT syndrome 10

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 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:: RCV003604780.1

Allele description

NM_174934.4(SCN4B):c.305C>A (p.Thr102Asn)

Genes:

LOC126861356:BRD4-independent group 4 enhancer GRCh37_chr11:118014519-118015718 [Gene]
SCN4B:sodium voltage-gated channel beta subunit 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_174934.4(SCN4B):c.305C>A (p.Thr102Asn)

HGVS:

NC_000011.10:g.118143991G>T
NG_011710.1:g.13925C>A
NG_085855.1:g.288G>T
NM_001142348.2:c.62-2655C>A
NM_001142349.2:c.-26C>A
NM_174934.4:c.305C>AMANE SELECT
NP_777594.1:p.Thr102Asn
NP_777594.1:p.Thr102Asn
LRG_330t1:c.305C>A
LRG_330:g.13925C>A
LRG_330p1:p.Thr102Asn
NC_000011.9:g.118014706G>T
NM_174934.3:c.305C>A
NR_024527.2:n.448C>A

Protein change:

T102N

Molecular consequence:

NM_001142349.2:c.-26C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001142348.2:c.62-2655C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_174934.4:c.305C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_024527.2:n.448C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Long QT syndrome 10 (LQT10)
Identifiers:: MONDO: MONDO:0012737; MedGen: C2678484; Orphanet: 101016; Orphanet: 768; OMIM: 611819

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004504456	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 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

SCV004504456

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 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

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, SCV004504456.1

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

Description

This sequence change replaces threonine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 102 of the SCN4B protein (p.Thr102Asn). This variant is not present in population databases (gnomAD no frequency). 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 tolerated. This variant has not been reported in the literature in individuals affected with SCN4B-related conditions.

#	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: Feb 28, 2024

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