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NM_000335.5(SCN5A):c.568C>G (p.Arg190Gly) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Dec 20, 2023
Review status:
criteria provided, conflicting classifications
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:
RCV000766778.11

Allele description [Variation Report for NM_000335.5(SCN5A):c.568C>G (p.Arg190Gly)]

NM_000335.5(SCN5A):c.568C>G (p.Arg190Gly)

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.568C>G (p.Arg190Gly)
Other names:
p.R190G:CGG>GGG
HGVS:
  • NC_000003.12:g.38620886G>C
  • NG_008934.1:g.33787C>G
  • NM_000335.5:c.568C>GMANE SELECT
  • NM_001099404.2:c.568C>G
  • NM_001099405.2:c.568C>G
  • NM_001160160.2:c.568C>G
  • NM_001160161.2:c.568C>G
  • NM_001354701.2:c.568C>G
  • NM_198056.3:c.568C>G
  • NP_000326.2:p.Arg190Gly
  • NP_001092874.1:p.Arg190Gly
  • NP_001092875.1:p.Arg190Gly
  • NP_001153632.1:p.Arg190Gly
  • NP_001153633.1:p.Arg190Gly
  • NP_001341630.1:p.Arg190Gly
  • NP_932173.1:p.Arg190Gly
  • NP_932173.1:p.Arg190Gly
  • LRG_289t1:c.568C>G
  • LRG_289:g.33787C>G
  • LRG_289p1:p.Arg190Gly
  • NC_000003.11:g.38662377G>C
  • NM_198056.2:c.568C>G
Protein change:
R190G
Links:
dbSNP: rs199473068
NCBI 1000 Genomes Browser:
rs199473068
Molecular consequence:
  • NM_000335.5:c.568C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099404.2:c.568C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099405.2:c.568C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160160.2:c.568C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160161.2:c.568C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354701.2:c.568C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198056.3:c.568C>G - 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
SCV000235327GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Uncertain significance
(Oct 1, 2013)
germlineclinical testing

Citation Link,

SCV002403981Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Dec 20, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot 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

Details of each submission

From GeneDx, SCV000235327.10

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

Description

p.Arg190Gly (CGG>GGG): c.568 C>G in exon 5 of the SCN5A gene (NM_198056.2) The Arg190Gly variant in the SCN5A gene has been reported in three unrelated families from Finland with LQTS, however, it was present in 2/200 healthy Finnish controls (Fodstad H et al., 2004). Fodstad et al. concluded further studies are necessary to determine if Arg190Gly is associated with a LQTS phenotype or if it is a rare benign variant. Arg190Gly results in a non-conservative amino acid substitution of a positively charged Arginine with a non-polar Glycine at a position that is conserved across species. Other mutations in this residue (Arg190Gln) and in nearby residues (Thr187Ile, Ala204Val) have been reported in association with LQTS further supporting the functional importance of this residue and this region of the protein. Furthermore, the Arg190Gly variant was not observed inapproximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. With the clinical and molecular information available at this time, we cannot definitively determine if Arg190Gly is a disease-causing mutation or a rare benign variant. The variant is found in LQT panel(s).

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002403981.3

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

Last Updated: Oct 26, 2024