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NM_000335.5(SCN5A):c.5371G>T (p.Asp1791Tyr) AND Cardiac arrhythmia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 18, 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:
RCV004015584.2

Allele description [Variation Report for NM_000335.5(SCN5A):c.5371G>T (p.Asp1791Tyr)]

NM_000335.5(SCN5A):c.5371G>T (p.Asp1791Tyr)

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.5371G>T (p.Asp1791Tyr)
HGVS:
  • NC_000003.12:g.38550998C>A
  • NG_008934.1:g.103675G>T
  • NM_000335.5:c.5371G>TMANE SELECT
  • NM_001099404.2:c.5374G>T
  • NM_001099405.2:c.5320G>T
  • NM_001160160.2:c.5275G>T
  • NM_001160161.2:c.5212G>T
  • NM_001354701.2:c.5317G>T
  • NM_198056.3:c.5374G>T
  • NP_000326.2:p.Asp1791Tyr
  • NP_000326.2:p.Asp1791Tyr
  • NP_001092874.1:p.Asp1792Tyr
  • NP_001092874.1:p.Asp1792Tyr
  • NP_001092875.1:p.Asp1774Tyr
  • NP_001153632.1:p.Asp1759Tyr
  • NP_001153633.1:p.Asp1738Tyr
  • NP_001341630.1:p.Asp1773Tyr
  • NP_932173.1:p.Asp1792Tyr
  • NP_932173.1:p.Asp1792Tyr
  • LRG_289t1:c.5374G>T
  • LRG_289t2:c.5371G>T
  • LRG_289t3:c.5374G>T
  • LRG_289:g.103675G>T
  • LRG_289p1:p.Asp1792Tyr
  • LRG_289p2:p.Asp1791Tyr
  • LRG_289p3:p.Asp1792Tyr
  • NC_000003.11:g.38592489C>A
  • NM_000335.4:c.5371G>T
  • NM_001099404.1:c.5374G>T
  • NM_198056.2:c.5374G>T
  • NR_176299.1:n.6120G>T
Protein change:
D1738Y
Molecular consequence:
  • NM_000335.5:c.5371G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099404.2:c.5374G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099405.2:c.5320G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160160.2:c.5275G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160161.2:c.5212G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354701.2:c.5317G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198056.3:c.5374G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_176299.1:n.6120G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
2

Condition(s)

Name:
Cardiac arrhythmia
Synonyms:
Cardiac rhythm disease
Identifiers:
EFO: EFO_0004269; MONDO: MONDO:0007263; MedGen: C0003811; Human Phenotype Ontology: HP:0011675

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004838383All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain Significance
(Dec 18, 2023) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown2not providednot provided108544not providedclinical testing

Citations

PubMed

Enhancing rare variant interpretation in inherited arrhythmias through quantitative analysis of consortium disease cohorts and population controls.

Walsh R, Lahrouchi N, Tadros R, Kyndt F, Glinge C, Postema PG, Amin AS, Nannenberg EA, Ware JS, Whiffin N, Mazzarotto F, Škorić-Milosavljević D, Krijger C, Arbelo E, Babuty D, Barajas-Martinez H, Beckmann BM, Bézieau S, Bos JM, Breckpot J, Campuzano O, Castelletti S, et al.

Genet Med. 2021 Jan;23(1):47-58. doi: 10.1038/s41436-020-00946-5. Epub 2020 Sep 7.

PubMed [citation]
PMID:
32893267
PMCID:
PMC7790744

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 All of Us Research Program, National Institutes of Health, SCV004838383.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (2)

Description

This missense variant replaces aspartic acid with tyrosine at codon 1792 of the SCN5A protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). This variant is found within a highly conserved C-terminus domain (a.a. 1772-2016). Rare non-truncating variants in this region have been shown to be significantly overrepresented in individuals with Brugada syndrome and long QT syndrome (PMID: 32893267). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with SCN5A-related disorders in the literature. This variant has been identified in 1/250584 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided2not providednot providednot provided

Last Updated: May 7, 2024