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NM_000335.5(SCN5A):c.1197G>A (p.Leu399=) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jan 18, 2022
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:
RCV001508496.7

Allele description [Variation Report for NM_000335.5(SCN5A):c.1197G>A (p.Leu399=)]

NM_000335.5(SCN5A):c.1197G>A (p.Leu399=)

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.1197G>A (p.Leu399=)
HGVS:
  • NC_000003.12:g.38606092C>T
  • NG_008934.1:g.48581G>A
  • NM_000335.5:c.1197G>AMANE SELECT
  • NM_001099404.2:c.1197G>A
  • NM_001099405.2:c.1197G>A
  • NM_001160160.2:c.1197G>A
  • NM_001160161.2:c.1197G>A
  • NM_001354701.2:c.1197G>A
  • NM_198056.3:c.1197G>A
  • NP_000326.2:p.Leu399=
  • NP_001092874.1:p.Leu399=
  • NP_001092875.1:p.Leu399=
  • NP_001153632.1:p.Leu399=
  • NP_001153633.1:p.Leu399=
  • NP_001341630.1:p.Leu399=
  • NP_932173.1:p.Leu399=
  • LRG_289t1:c.1197G>A
  • LRG_289:g.48581G>A
  • NC_000003.11:g.38647583C>T
  • NM_198056.2:c.1197G>A
  • p.Leu399=
Links:
dbSNP: rs763205210
NCBI 1000 Genomes Browser:
rs763205210
Molecular consequence:
  • NM_000335.5:c.1197G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001099404.2:c.1197G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001099405.2:c.1197G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001160160.2:c.1197G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001160161.2:c.1197G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354701.2:c.1197G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_198056.3:c.1197G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001387216Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 18, 2022) 		germlineclinical testing

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

SCV001714696Mayo Clinic Laboratories, Mayo Clinic
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 10, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical 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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001387216.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 944955). This variant has been observed in individual(s) with clinical features of SCN5A-related conditions (Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change affects codon 399 of the SCN5A mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the SCN5A protein.

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

From Mayo Clinic Laboratories, Mayo Clinic, SCV001714696.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 10, 2024