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NM_000335.5(SCN5A):c.3748G>A (p.Val1250Met) AND not provided

Germline classification:
Likely benign (6 submissions)
Last evaluated:
Jan 24, 2024
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:
RCV000058599.24

Allele description [Variation Report for NM_000335.5(SCN5A):c.3748G>A (p.Val1250Met)]

NM_000335.5(SCN5A):c.3748G>A (p.Val1250Met)

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.3748G>A (p.Val1250Met)
Other names:
p.V1251M:GTG>ATG
HGVS:
  • NC_000003.12:g.38566498C>T
  • NG_008934.1:g.88175G>A
  • NM_000335.5:c.3748G>AMANE SELECT
  • NM_001099404.2:c.3751G>A
  • NM_001099405.2:c.3751G>A
  • NM_001160160.2:c.3748G>A
  • NM_001160161.2:c.3589G>A
  • NM_001354701.2:c.3748G>A
  • NM_198056.3:c.3751G>A
  • NP_000326.2:p.Val1250Met
  • NP_001092874.1:p.Val1251Met
  • NP_001092875.1:p.Val1251Met
  • NP_001153632.1:p.Val1250Met
  • NP_001153633.1:p.Val1197Met
  • NP_001341630.1:p.Val1250Met
  • NP_932173.1:p.Val1251Met
  • NP_932173.1:p.Val1251Met
  • LRG_289t1:c.3751G>A
  • LRG_289:g.88175G>A
  • LRG_289p1:p.Val1251Met
  • NC_000003.11:g.38607989C>T
  • NM_198056.2:c.3751G>A
  • Q14524:p.Val1251Met
Protein change:
V1197M
Links:
UniProtKB: Q14524#VAR_074418; dbSNP: rs199473600
NCBI 1000 Genomes Browser:
rs199473600
Molecular consequence:
  • NM_000335.5:c.3748G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099404.2:c.3751G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099405.2:c.3751G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160160.2:c.3748G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160161.2:c.3589G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354701.2:c.3748G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198056.3:c.3751G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000090119Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust
no classification provided
not providedgermlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV000235603GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely benign
(Jan 14, 2021)
germlineclinical testing

Citation Link,

SCV000291806Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 24, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000924957Stanford Center for Inherited Cardiovascular Disease, Stanford University
no assertion criteria provided
Uncertain significance
(Jun 20, 2016)
germlineprovider interpretation

SCV001922810Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Likely benigngermlineclinical testing

SCV001951593Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Likely benigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, literature only, provider interpretation

Citations

PubMed

Genetic testing for long-QT syndrome: distinguishing pathogenic mutations from benign variants.

Kapa S, Tester DJ, Salisbury BA, Harris-Kerr C, Pungliya MS, Alders M, Wilde AA, Ackerman MJ.

Circulation. 2009 Nov 3;120(18):1752-60. doi: 10.1161/CIRCULATIONAHA.109.863076. Epub 2009 Oct 19.

PubMed [citation]
PMID:
19841300
PMCID:
PMC3025752

An international compendium of mutations in the SCN5A-encoded cardiac sodium channel in patients referred for Brugada syndrome genetic testing.

Kapplinger JD, Tester DJ, Alders M, Benito B, Berthet M, Brugada J, Brugada P, Fressart V, Guerchicoff A, Harris-Kerr C, Kamakura S, Kyndt F, Koopmann TT, Miyamoto Y, Pfeiffer R, Pollevick GD, Probst V, Zumhagen S, Vatta M, Towbin JA, Shimizu W, Schulze-Bahr E, et al.

Heart Rhythm. 2010 Jan;7(1):33-46. doi: 10.1016/j.hrthm.2009.09.069. Epub 2009 Oct 8.

PubMed [citation]
PMID:
20129283
PMCID:
PMC2822446
See all PubMed Citations (4)

Details of each submission

From Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust, SCV000090119.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

This variant has been reported in the following publications (PMID:19841300;PMID:20129283).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV000235603.12

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is associated with the following publications: (PMID: 19841300, 20129283, 15851227, 26746457, 25904541)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000291806.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Stanford Center for Inherited Cardiovascular Disease, Stanford University, SCV000924957.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedprovider interpretationnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001922810.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001951593.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024